Initial commit with LFS

.gitignore

@@ -0,0 +1,17 @@
+entangled-tps/results/
+entangled-tps/scripts/wandb/
+entangled-tps/scripts/logs/
+entangled-tps/scripts/results/
+entangled-tps/wandb/
+entangled-tps/logs/
+entangled-cell/__pycache__/
+entangled-cell/scripts/lightning_logs/
+entangled-cell/logs/
+entangled-cell/results/
+entangled-cell/scripts/wandb/
+entangled-cell/wandb/
+*.pt
+*.log
+*.ckpt
+*.pyc
+*.npy

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Sophia Tang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,51 @@
+# [Entangled Schrödinger Bridge Matching](https://arxiv.org/abs/2511.07406v1) ⚛️🌟
+
+
+[**Sophia Tang**](https://sophtang.github.io/), **[Yinuo Zhang](https://www.linkedin.com/in/yinuozhang98/)**, and [**Pranam Chatterjee**](https://www.chatterjeelab.com/)
+
+![EntangledSBM](assets/entangled.gif)
+
+This is the repository for **Entangled Schrödinger Bridge Matching** ⚛️🌟. It is partially built on the [**BranchSBM repo**](https://huggingface.co/ChatterjeeLab/BranchSBM) ([Tang et al. 2025](https://arxiv.org/abs/2506.09007)), the [**TPS-DPS repo**](https://github.com/kiyoung98/tps-dps) ([Seong et al. 2024](https://arxiv.org/abs/2405.19961)), and the [**Metric Flow Matching repo**](https://github.com/kkapusniak/metric-flow-matching) ([Kapusniak et al. 2024](https://arxiv.org/abs/2405.14780)).
+
+Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Flow and Schrödinger bridge matching have been used to implicitly learn joint trajectories through data snapshots. However, many systems undergo *dynamic interactions* that evolve over their trajectory and cannot be captured through static snapshots.
+
+**EntangledSBM** solves this by learning the first- and second-order stochastic dynamics of interacting, multi-particle systems where the direction and magnitude of each particle’s path depend dynamically on the paths of the other particles.  
+
+🌟 We formulate the **Entangled Schrödinger Bridge (EntangledSB) problem** that aims to parameterize a **bias force** that dynamically depends on the system’s positions and velocities as they evolve over time. 
+
+🌟 To solve the EntangledSB problem, we introduce a novel parameterization of the bias force that can be conditioned, *at inference time*, on a target distribution or terminal state, enabling the generation of trajectories to **diverse target distributions.**
+
+🌟 We minimize the divergence of the simulated path distribution from the optimal bridge distribution using a **weighted cross-entropy** objective. 
+
+We evaluate EntangledSBM on **mapping cell cluster dynamics under drug perturbations** and **transition path sampling (TPS) of high-dimensional molecular systems.**
+
+## Cell-State Perturbation Experiment 🧫
+
+In this experiment, we evaluate the ability of EntangledSBM to **generate the trajectories of cell clusters under perturbation**. We demonstrate that EntanlgedSBM accurately **reconstructs perturbed cell states** and **generalizes to divergent target states not seen during training**. 
+
+Code and instructions to reproduce our results are provided in `/entangled-cell`.
+
+![EntangledSBM for Cell Perturbation Modelling](assets/fig-trametinib.png)
+
+## Transition Path Sampling Experiment ⚛️
+
+In this experiment, we evaluate the capability of EntangledSBM in **simulating molecular dynamics (MD) trajectories** given a potential energy landscape and the starting and target metastable states. We evaluate Alanine Dipeptide and three fast-folding proteins (Chignolin, Trp-cage, and BBA) and demonstrate enhanced performance against baselines for all-atom simulations. 
+
+Code and instructions to reproduce our results are provided in `/entangled-tps`.
+
+![EntangledSBM for Transition Path Sampling](assets/tps-full.png)
+
+## Citation
+
+If you find this repository helpful for your publications, please consider citing our paper:
+
+```python
+@article{tang2025entangledsbm,
+  title={Entangled Schrödinger Bridge Matching},
+  author={Sophia Tang and Yinuo Zhang and Pranam Chatterjee},
+  journal={arXiv preprint arXiv:2511.07406},
+  year={2025}
+}
+```
+
+To use this repository, you agree to abide by the MIT License.

entangled-cell/README.md

@@ -0,0 +1,89 @@
+# EntangledSBM for Cell Perturbation Modelling 🧫
+
+This part of the code is for running the cell perturbation experiments. We demonstrate that EntanlgedSBM accurately **reconstructs perturbed cell states** and **generalizes to divergent target states not seen during training**. This codebase is partially built off of the [BranchSBM repo](https://github.com/kiyoung98/tps-dps/tree/main) ([Tang et al. 2025](https://arxiv.org/abs/2506.09007)) and the [Metric Flow Matching repo](https://github.com/kkapusniak/metric-flow-matching) ([Kapusniak et al. 2024](https://arxiv.org/abs/2405.14780)).
+
+## Environment Installation
+```
+conda env create -f environment.yml
+
+conda activate entangled-cell
+```
+
+## Data
+
+We use perturbation data from the [Tahoe-100M dataset](https://huggingface.co/datasets/tahoebio/Tahoe-100M) containing control DMSO-treated cell data and perturbed cell data. 
+
+The raw data contains a total of 60K genes. We select the top 2000 highly variable genes (HVGs) and perform principal component analysis (PCA), to maximally capture the variance in the data via the top principal components (38% in the top-50 PCs). **Our goal is to learn the dynamic trajectories that map control cell clusters to the perturbd cell clusters.**
+
+**Specifically, we model the following perturbations**:
+
+1. **Clonidine**: Cell states under 5uM Clonidine perturbation at various PC dimensions (50D, 100D, 150D) with 1 unseen population.
+2. **Trametinib**: Cell states under 5uM Trametinib perturbation (50D) with 2 unseen populations.
+
+Processed data files are stored in:
+```
+entangled-cell/data/
+├── pca_and_leiden_labels.csv              # Clonidine data
+└── Trametinib_5.0uM_pca_and_leidenumap_labels.csv  # Trametinib data
+```
+
+## Running Experiments
+
+All training scripts are located in `entangled-cell/scripts/`. Each script is pre-configured for a specific experiment.
+
+**Before running experiments:**
+
+1. Set `HOME_LOC` to the base path where EntangledSBM is located and `ENV_PATH` to the directory where your environment is downloaded in the `.sh` files in `scripts/`
+2. Create a path `entangled-cell/results` where the simulated trajectory figures and metrics will be saved. Also, create `entangled-cell/logs` where the training logs will be saved.
+3. Activate the conda environment:
+```
+conda activate entangled-cell
+```
+4. Login to wandb using `wandb login`
+
+**Run experiment using `nohup` with the following commands:**
+
+```
+cd entangled-cell/scripts
+
+chmod clonidine50.sh
+
+nohup ./clonidine50.sh > clonidine50.log 2>&1 &
+```
+Evaluation will run automatically after the specified number of rollouts `--num_rollouts` is finished. To see metrics, go to `results/<experiment>/metrics/` or the end of `logs/<experiment>.log`. 
+
+For Clonidine, `x1_1` indicates the cell cluster that is sampled from for training and `x1_2` is the held-out cell cluster. For Trametinib `x1_1` indicates the cell cluster that is sampled from for training and `x1_2` and `x1_3` are the held-out cell clusters.
+
+We report the following metrics for each of the clusters in our paper:
+1. Maximum Mean Discrepancy (RBF-MMD) of simualted cell cluster with target cell cluster (same cell count).
+2. 1-Wasserstein and 2-Wasserstein distances against full cell population in the cluster.
+
+## Overview of Outputs
+
+**Training outputs are saved to experiment-specific directories:**
+
+```
+entangled-cell/results/
+├── clonidine_ce_50D/
+│   └── positions/         # Generated trajectory
+│   └── metrics/         # JSON of metrics
+│   └── figures/         # Figures of simulated trajectories
+```
+
+**PyTorch Lightning automatically saves model checkpoints to:**
+
+```
+entangled-cell/scripts/lightning_logs/
+├── <wandb-run-id>/
+│   ├── checkpoints/
+│   │   ├── epoch=N-step=M.ckpt     # Checkpoint 
+```
+
+**Training logs are saved in:**
+```
+entangled-cell/logs/
+├── <DATE>_clonidine-ce-50D_train.log
+├── <DATE>_clonidine-ce-100D_train.log
+├── <DATE>_clonidine-ce-150D_train.log
+└── <DATE>_trametinib-ce-50D_train.log
+```

entangled-cell/bias.py

@@ -0,0 +1,187 @@
+import sys
+import os
+os.environ["CUDA_VISIBLE_DEVICES"] = "6"
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+class BiasForceTransformer(nn.Module):
+    def __init__(self,
+                 args,
+                 d_model = 256,
+                 nhead = 8,
+                 num_layers = 4,
+                 dim_feedforward = 512,
+                 dropout = 0.1,
+                 ):
+        super().__init__()
+        self.device = args.device
+        self.N = args.num_particles
+        
+        self.use_delta_to_target = args.use_delta_to_target
+        self.rbf = args.rbf
+        
+        self.sigma = args.sigma
+
+        G = args.dim
+        # Per-atom features in aligned frame for the Transformer
+        # pos_al(3), vel_al(3), delta_to_target(3 optional), distance(1)
+        feat_dim = (2 * G) + (G if self.use_delta_to_target else 0) + 1
+
+        self.input_proj = nn.Linear(feat_dim, d_model)
+        enc_layer = nn.TransformerEncoderLayer(
+            d_model=d_model, nhead=nhead,
+            dim_feedforward=dim_feedforward,
+            dropout=dropout, activation="gelu",
+            batch_first=True, norm_first=True
+        )
+        self.encoder = nn.TransformerEncoder(enc_layer, num_layers=num_layers)
+
+        # Heads
+        self.scale_head = nn.Sequential(
+            nn.Linear(d_model, d_model // 2),
+            nn.GELU(),
+            nn.Linear(d_model // 2, 1),
+        )
+        self.vec_head = nn.Sequential(
+            nn.Linear(d_model, d_model // 2),
+            nn.GELU(),
+            nn.Linear(d_model // 2, args.dim),
+        )
+
+        self.log_z = nn.Parameter(torch.tensor(0.0))
+        #self.to(self.device)
+
+    @staticmethod
+    def _softplus_unit(x, beta=1.0, threshold=20.0, eps=1e-8):
+        return F.softplus(x, beta=beta, threshold=threshold) + eps
+
+    def forward(self, pos, vel, target):
+        """
+        pos, vel, target: (B,N,D)
+        Returns: force (B,N,D), scale (B,N), vector (B,N,D)
+        
+        N: number of cells in batch
+        D: dimension of gene vector
+        """
+        B, N, G = pos.shape
+        assert N == self.N, f"Expected N={self.N}, got {N}"
+
+        # direction of target position
+        delta = target - pos # (B,N,G)
+        dist  = torch.norm(delta, dim=-1, keepdim=True)  # (B,N,1)
+        feats = torch.cat([pos, vel, delta, dist], dim=-1) \
+                if self.use_delta_to_target else torch.cat([pos, vel, dist], dim=-1)
+
+        x = self.input_proj(feats) # (B,N,d_model)
+        x = self.encoder(x) # (B,N,d_model)
+
+        # Heads
+        scale = self._softplus_unit(self.scale_head(x)).squeeze(-1)     # (B,N)
+        vector = self.vec_head(x)                          # (B,N,3)
+
+        # Direction field d
+        d = (target - pos)
+
+        # Parallel component from scale head
+        scale = scale.unsqueeze(-1).expand(-1, -1, G) 
+        scaled = scale * d # (B,N,3)
+
+        # Project vector head output onto plane orthogonal to d
+        eps = torch.finfo(pos.dtype).eps
+        denom = d.pow(2).sum(dim=-1, keepdim=True).clamp_min(eps)        # (B,N,1)
+        vec_parallel = ((vector * d).sum(dim=-1, keepdim=True) / denom) * d
+        vec_perp = vector - vec_parallel
+
+        return vec_perp + scaled 
+    
+class BiasForceTransformerNoVel(nn.Module):
+    def __init__(self,
+                 args,
+                 d_model = 256,
+                 nhead = 8,
+                 num_layers = 4,
+                 dim_feedforward = 512,
+                 dropout = 0.1,
+                 ):
+        super().__init__()
+        self.device = args.device
+        self.N = args.num_particles
+        
+        self.use_delta_to_target = args.use_delta_to_target
+        self.rbf = args.rbf
+        
+        self.sigma = args.sigma
+
+        G = args.dim
+        # Per-atom features in aligned frame for the Transformer
+        # pos_al(3), vel_al(3), delta_to_target(3 optional), distance(1)
+        feat_dim = G + (G if self.use_delta_to_target else 0) + 1
+
+        self.input_proj = nn.Linear(feat_dim, d_model)
+        enc_layer = nn.TransformerEncoderLayer(
+            d_model=d_model, nhead=nhead,
+            dim_feedforward=dim_feedforward,
+            dropout=dropout, activation="gelu",
+            batch_first=True, norm_first=True
+        )
+        self.encoder = nn.TransformerEncoder(enc_layer, num_layers=num_layers)
+
+        # Heads
+        self.scale_head = nn.Sequential(
+            nn.Linear(d_model, d_model // 2),
+            nn.GELU(),
+            nn.Linear(d_model // 2, 1),
+        )
+        self.vec_head = nn.Sequential(
+            nn.Linear(d_model, d_model // 2),
+            nn.GELU(),
+            nn.Linear(d_model // 2, args.dim),
+        )
+
+        self.log_z = nn.Parameter(torch.tensor(0.0))
+        #self.to(self.device)
+
+    @staticmethod
+    def _softplus_unit(x, beta=1.0, threshold=20.0, eps=1e-8):
+        return F.softplus(x, beta=beta, threshold=threshold) + eps
+
+    def forward(self, pos, target):
+        """
+        pos, target: (B,N,D)
+        Returns: force (B,N,D), scale (B,N), vector (B,N,D)
+        
+        N: number of cells in batch
+        D: dimension of gene vector
+        """
+        B, N, G = pos.shape
+        assert N == self.N, f"Expected N={self.N}, got {N}"
+
+        # direction of target position
+        delta = target - pos # (B,N,G)
+        dist  = torch.norm(delta, dim=-1, keepdim=True)  # (B,N,1)
+        feats = torch.cat([pos, delta, dist], dim=-1) \
+                if self.use_delta_to_target else torch.cat([pos, dist], dim=-1)
+
+        x = self.input_proj(feats) # (B,N,d_model)
+        x = self.encoder(x) # (B,N,d_model)
+
+        # Heads
+        scale = self._softplus_unit(self.scale_head(x)).squeeze(-1)     # (B,N)
+        vector = self.vec_head(x)                          # (B,N,3)
+
+        # Direction field d
+        d = (target - pos)
+
+        # Parallel component from scale head
+        scale = scale.unsqueeze(-1).expand(-1, -1, G) 
+        scaled = scale * d # (B,N,3)
+
+        # Project vector head output onto plane orthogonal to d
+        eps = torch.finfo(pos.dtype).eps
+        denom = d.pow(2).sum(dim=-1, keepdim=True).clamp_min(eps)        # (B,N,1)
+        vec_parallel = ((vector * d).sum(dim=-1, keepdim=True) / denom) * d
+        vec_perp = vector - vec_parallel
+
+        return vec_perp + scaled 

entangled-cell/configs/clonidine_100D.yaml

@@ -0,0 +1,11 @@
+data_type: "tahoe"
+data_name: "clonidine100D"
+accelerator: "gpu"
+dim: 100
+velocity_metric: "rbf"
+metric_patience: 25
+n_centers: 300
+kappa: 2
+rho: -2.75
+alpha_metric: 1
+metric_epochs: 400

entangled-cell/configs/clonidine_150D.yaml

@@ -0,0 +1,11 @@
+data_type: "tahoe"
+data_name: "clonidine150D"
+accelerator: "gpu"
+dim: 150
+velocity_metric: "rbf"
+metric_patience: 25
+n_centers: 300
+kappa: 3
+rho: -2.75
+alpha_metric: 1
+metric_epochs: 400

entangled-cell/configs/clonidine_50D.yaml

@@ -0,0 +1,11 @@
+data_type: "tahoe"
+data_name: "clonidine50Dsingle"
+dim: 50
+velocity_metric: "rbf"
+metric_patience: 25
+n_centers: 150
+kappa: 1.5
+rho: -2.75
+alpha_metric: 1
+metric_epochs: 200
+accelerator: "gpu"

entangled-cell/configs/trametinib_50D.yaml

@@ -0,0 +1,11 @@
+data_type: "tahoe"
+data_name: "trametinib"
+accelerator: "gpu"
+dim: 50
+velocity_metric: "rbf"
+metric_patience: 25
+n_centers: 150
+kappa: 1.5
+rho: -2.75
+alpha_metric: 1
+metric_epochs: 200

entangled-cell/data/Trametinib_5.0uM_pca_and_leidenumap_labels.csv

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+version https://git-lfs.github.com/spec/v1
+oid sha256:1c8cda9ec3b589e99db0d7b48a8d004d6dff159a2c5c253e604e93eb95e0f723
+size 40651087

entangled-cell/data/pca_and_leiden_labels.csv

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d63d8d2732d227be59d1106e456a9caad4b016972492e08e73f29a9d7226e805
+size 271796108

entangled-cell/data/rainier2-thin.las

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+version https://git-lfs.github.com/spec/v1
+oid sha256:246c3f3f7d25bfb5fa0a6f2500b9fe12b88f0985b8bae8f9529eb89c6efc68e0
+size 1878303

entangled-cell/dataloaders/clonidine_v2_data.py

@@ -0,0 +1,316 @@
+import torch
+import sys
+from sklearn.preprocessing import StandardScaler
+import pytorch_lightning as pl
+from torch.utils.data import DataLoader
+from lightning.pytorch.utilities.combined_loader import CombinedLoader
+import pandas as pd
+import numpy as np
+from functools import partial
+from scipy.spatial import cKDTree
+from sklearn.cluster import KMeans
+from torch.utils.data import TensorDataset
+
+class ClonidineV2DataModule(pl.LightningDataModule):
+    def __init__(self, args):
+        super().__init__()
+        self.save_hyperparameters()
+
+        self.batch_size = args.batch_size
+        self.max_dim = args.dim
+        #self.whiten = args.whiten
+        self.split_ratios = args.split_ratios
+        
+        self.dim = args.dim
+        # Path to your combined data
+        self.data_path = f"{args.root_dir}/data/pca_and_leiden_labels.csv"
+        self.num_timesteps = 2
+        self.args = args
+        self._prepare_data()
+
+    def _prepare_data(self):
+        df = pd.read_csv(self.data_path, comment='#')
+        df = df.iloc[:, 1:]
+        df = df.replace('', np.nan)
+        pc_cols = df.columns[:self.dim]
+        for col in pc_cols:
+            df[col] = pd.to_numeric(df[col], errors='coerce')
+        leiden_dmso_col = 'leiden_DMSO_TF_0.0uM'
+        leiden_clonidine_col = 'leiden_Clonidine (hydrochloride)_5.0uM'
+
+        dmso_mask = df[leiden_dmso_col].notna()        # Has leiden value in DMSO column
+        clonidine_mask = df[leiden_clonidine_col].notna()  # Has leiden value in Clonidine column
+        
+        dmso_data = df[dmso_mask].copy()
+        clonidine_data = df[clonidine_mask].copy()
+        
+        top_clonidine_clusters = ['0.0', '4.0']
+        
+        x1_1_data = clonidine_data[clonidine_data[leiden_clonidine_col].astype(str) == top_clonidine_clusters[0]]
+        x1_2_data = clonidine_data[clonidine_data[leiden_clonidine_col].astype(str) == top_clonidine_clusters[1]]
+        
+        x1_1_coords = x1_1_data[pc_cols].values 
+        x1_2_coords = x1_2_data[pc_cols].values 
+        
+        x1_1_coords = x1_1_coords.astype(float)
+        x1_2_coords = x1_2_coords.astype(float)
+
+        # Target size is now the minimum across all three endpoint clusters
+        target_size = min(len(x1_1_coords), len(x1_2_coords),)
+        
+        # Helper function to select points closest to centroid
+        def select_closest_to_centroid(coords, target_size):
+            if len(coords) <= target_size:
+                return coords
+            
+            # Calculate centroid
+            centroid = np.mean(coords, axis=0)
+            
+            # Calculate distances to centroid
+            distances = np.linalg.norm(coords - centroid, axis=1)
+            
+            # Get indices of closest points
+            closest_indices = np.argsort(distances)[:target_size]
+            
+            return coords[closest_indices]
+        
+        # Sample all endpoint clusters to target size using centroid-based selection
+        x1_1_coords = select_closest_to_centroid(x1_1_coords, target_size)
+        x1_2_coords = select_closest_to_centroid(x1_2_coords, target_size)
+        
+        dmso_cluster_counts = dmso_data[leiden_dmso_col].value_counts()
+        
+        # DMSO (unchanged)
+        largest_dmso_cluster = dmso_cluster_counts.index[0]
+        dmso_cluster_data = dmso_data[dmso_data[leiden_dmso_col] == largest_dmso_cluster]
+        
+        dmso_coords = dmso_cluster_data[pc_cols].values
+        
+        # Random sampling from largest DMSO cluster to match target size
+        # For DMSO, we'll also use centroid-based selection for consistency
+        if len(dmso_coords) >= target_size:
+            x0_coords = select_closest_to_centroid(dmso_coords, target_size)
+        else:
+            # If largest cluster is smaller than target, use all of it and pad with other DMSO cells
+            remaining_needed = target_size - len(dmso_coords)
+            other_dmso_data = dmso_data[dmso_data[leiden_dmso_col] != largest_dmso_cluster]
+            other_dmso_coords = other_dmso_data[pc_cols].values
+            
+            if len(other_dmso_coords) >= remaining_needed:
+                # Select closest to centroid from other DMSO cells
+                other_selected = select_closest_to_centroid(other_dmso_coords, remaining_needed)
+                x0_coords = np.vstack([dmso_coords, other_selected])
+            else:
+                # Use all available DMSO cells and reduce target size
+                all_dmso_coords = dmso_data[pc_cols].values
+                target_size = min(target_size, len(all_dmso_coords))
+                x0_coords = select_closest_to_centroid(all_dmso_coords, target_size)
+                
+                # Re-select endpoint clusters with updated target size
+                x1_1_coords = select_closest_to_centroid(x1_1_data[pc_cols].values.astype(float), target_size)
+                x1_2_coords = select_closest_to_centroid(x1_2_data[pc_cols].values.astype(float), target_size)
+        
+        # No need to resample since we already selected the right number
+        # The endpoint clusters are already at target_size from centroid-based selection
+        
+        self.n_samples = target_size
+        
+        x0 = torch.tensor(x0_coords, dtype=torch.float32)
+        x1_1 = torch.tensor(x1_1_coords, dtype=torch.float32)
+        x1_2 = torch.tensor(x1_2_coords, dtype=torch.float32)
+        
+        self.coords_t0 = x0
+        self.coords_t1_1 = x1_1
+        self.coords_t1_2 = x1_2
+        self.time_labels = np.concatenate([
+            np.zeros(len(self.coords_t0)),    # t=0
+            np.ones(len(self.coords_t1_1)),     # t=1
+            np.ones(len(self.coords_t1_2)),
+        ])
+        
+        split_index = int(target_size * self.split_ratios[0])
+        
+        if target_size - split_index < self.batch_size:
+            split_index = target_size - self.batch_size
+        
+        train_x0 = x0[:split_index]
+        val_x0 = x0[split_index:]
+        train_x1_1 = x1_1[:split_index]
+        val_x1_1 = x1_1[split_index:]
+        train_x1_2 = x1_2[:split_index]
+        val_x1_2 = x1_2[split_index:]
+
+        
+        self.val_x0 = val_x0
+        self.val_x1_1 = val_x1_1
+        self.val_x1_2 = val_x1_2
+        
+        train_x0_weights = torch.full((train_x0.shape[0], 1), fill_value=1.0)
+        train_x1_1_weights = torch.full((train_x1_1.shape[0], 1), fill_value=0.5)
+        train_x1_2_weights = torch.full((train_x1_2.shape[0], 1), fill_value=0.5)
+        
+        val_x0_weights = torch.full((val_x0.shape[0], 1), fill_value=1.0)
+        val_x1_1_weights = torch.full((val_x1_1.shape[0], 1), fill_value=0.5)
+        val_x1_2_weights = torch.full((val_x1_2.shape[0], 1), fill_value=0.5)
+        
+        # Updated train dataloaders to include x1_3
+        self.train_dataloaders = {
+            "x0": DataLoader(TensorDataset(train_x0, train_x0_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_1": DataLoader(TensorDataset(train_x1_1, train_x1_1_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(train_x1_2, train_x1_2_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+        }
+        
+        self.val_dataloaders = {
+            "x0": DataLoader(TensorDataset(val_x0, val_x0_weights), batch_size=self.batch_size, shuffle=False, drop_last=True),
+            "x1_1": DataLoader(TensorDataset(val_x1_1, val_x1_1_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(val_x1_2, val_x1_2_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+        }
+        
+        all_coords = df[pc_cols].dropna().values.astype(float)
+        self.dataset = torch.tensor(all_coords, dtype=torch.float32)
+        self.tree = cKDTree(all_coords)
+
+        self.test_dataloaders = {
+            "x0": DataLoader(TensorDataset(val_x0, val_x0_weights), batch_size=self.val_x0.shape[0], shuffle=False, drop_last=False),
+            "x1_1": DataLoader(TensorDataset(val_x1_1, val_x1_1_weights), batch_size=self.val_x1_1.shape[0], shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(val_x1_2, val_x1_2_weights), batch_size=self.val_x1_2.shape[0], shuffle=True, drop_last=True),
+            "dataset": DataLoader(TensorDataset(self.dataset), batch_size=self.dataset.shape[0], shuffle=False, drop_last=False),
+        }
+
+        # Updated metric samples - now using 4 clusters instead of 3
+        #km_all = KMeans(n_clusters=4, random_state=42).fit(self.dataset.numpy())
+        """km_all = KMeans(n_clusters=3, random_state=0).fit(self.dataset.numpy())
+
+        cluster_labels = km_all.labels_
+        
+        cluster_0_mask = cluster_labels == 0
+        cluster_1_mask = cluster_labels == 1
+        cluster_2_mask = cluster_labels == 2
+        
+        samples = self.dataset.cpu().numpy()
+            
+        cluster_0_data = samples[cluster_0_mask]
+        cluster_1_data = samples[cluster_1_mask]
+        cluster_2_data = samples[cluster_2_mask]
+                
+        self.metric_samples_dataloaders = [
+            DataLoader(
+                torch.tensor(cluster_2_data, dtype=torch.float32),
+                batch_size=cluster_2_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            DataLoader(
+                torch.tensor(cluster_0_data, dtype=torch.float32),
+                batch_size=cluster_0_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            
+            DataLoader(
+                torch.tensor(cluster_1_data, dtype=torch.float32),
+                batch_size=cluster_1_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+        ]"""
+        
+        # Updated metric samples - now using 4 clusters instead of 3
+        #km_all = KMeans(n_clusters=4, random_state=42).fit(self.dataset.numpy())
+        km_all = KMeans(n_clusters=2, random_state=0).fit(self.dataset.numpy())
+
+        cluster_labels = km_all.labels_
+        
+        cluster_0_mask = cluster_labels == 0
+        cluster_1_mask = cluster_labels == 1
+        
+        samples = self.dataset.cpu().numpy()
+            
+        cluster_0_data = samples[cluster_0_mask]
+        cluster_1_data = samples[cluster_1_mask]
+                
+        self.metric_samples_dataloaders = [
+            DataLoader(
+                torch.tensor(cluster_1_data, dtype=torch.float32),
+                batch_size=cluster_1_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            DataLoader(
+                torch.tensor(cluster_0_data, dtype=torch.float32),
+                batch_size=cluster_0_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+        ]
+        
+    def train_dataloader(self):
+        combined_loaders = {
+            "train_samples": CombinedLoader(self.train_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    def val_dataloader(self):
+        combined_loaders = {
+            "val_samples": CombinedLoader(self.val_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    
+    
+    def test_dataloader(self):
+        combined_loaders = {
+            "test_samples": CombinedLoader(self.test_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    def get_manifold_proj(self, points):
+        """Adapted for 2D cell data - uses local neighborhood averaging instead of plane fitting"""
+        return partial(self.local_smoothing_op, tree=self.tree, dataset=self.dataset)
+
+    @staticmethod
+    def local_smoothing_op(x, tree, dataset, k=10, temp=1e-3):
+        """
+        Apply local smoothing based on k-nearest neighbors in the full dataset
+        This replaces the plane projection for 2D manifold regularization
+        """
+        points_np = x.detach().cpu().numpy()
+        _, idx = tree.query(points_np, k=k)
+        nearest_pts = dataset[idx]  # Shape: (batch_size, k, 2)
+        
+        # Compute weighted average of neighbors
+        dists = (x.unsqueeze(1) - nearest_pts).pow(2).sum(-1, keepdim=True)
+        weights = torch.exp(-dists / temp)
+        weights = weights / weights.sum(dim=1, keepdim=True)
+        
+        # Weighted average of neighbors
+        smoothed = (weights * nearest_pts).sum(dim=1)
+        
+        # Blend original point with smoothed version
+        alpha = 0.3  # How much smoothing to apply
+        return (1 - alpha) * x + alpha * smoothed
+    
+    def get_timepoint_data(self):
+        """Return data organized by timepoints for visualization"""
+        return {
+            't0': self.coords_t0,
+            't1_1': self.coords_t1_1, 
+            't1_2': self.coords_t1_2, 
+            'time_labels': self.time_labels
+        }
+    
+def get_datamodule():
+    datamodule = ClonidineV2DataModule(args)
+    datamodule.setup(stage="fit")   
+    return datamodule

entangled-cell/dataloaders/three_branch_data.py

@@ -0,0 +1,313 @@
+import torch
+import sys
+from sklearn.preprocessing import StandardScaler
+import pytorch_lightning as pl
+from torch.utils.data import DataLoader
+from lightning.pytorch.utilities.combined_loader import CombinedLoader
+import pandas as pd
+import numpy as np
+from functools import partial
+from scipy.spatial import cKDTree
+from sklearn.cluster import KMeans
+from torch.utils.data import TensorDataset
+
+class ThreeBranchTahoeDataModule(pl.LightningDataModule):
+    def __init__(self, args):
+        super().__init__()
+        self.save_hyperparameters()
+
+        self.batch_size = args.batch_size
+        self.max_dim = args.dim
+        self.split_ratios = args.split_ratios
+        self.num_timesteps = 2
+        self.data_path = f"{args.root_dir}/data/Trametinib_5.0uM_pca_and_leidenumap_labels.csv"
+        self.args = args
+
+        self._prepare_data()
+
+    def _prepare_data(self):
+        df = pd.read_csv(self.data_path, comment='#')
+        df = df.iloc[:, 1:]
+        df = df.replace('', np.nan)
+        pc_cols = df.columns[:50]
+        for col in pc_cols:
+            df[col] = pd.to_numeric(df[col], errors='coerce')
+        leiden_dmso_col = 'leiden_DMSO_TF_0.0uM'
+        leiden_clonidine_col = 'leiden_Trametinib_5.0uM'
+
+        dmso_mask = df[leiden_dmso_col].notna()        # Has leiden value in DMSO column
+        clonidine_mask = df[leiden_clonidine_col].notna()  # Has leiden value in Clonidine column
+        
+        dmso_data = df[dmso_mask].copy()
+        clonidine_data = df[clonidine_mask].copy()
+        
+        # Updated to include all three clusters: 0, 4, and 6
+        top_clonidine_clusters = ['1.0', '3.0', '5.0']
+        
+        x1_1_data = clonidine_data[clonidine_data[leiden_clonidine_col].astype(str) == top_clonidine_clusters[0]]
+        x1_2_data = clonidine_data[clonidine_data[leiden_clonidine_col].astype(str) == top_clonidine_clusters[1]]
+        x1_3_data = clonidine_data[clonidine_data[leiden_clonidine_col].astype(str) == top_clonidine_clusters[2]]
+        
+        x1_1_coords = x1_1_data[pc_cols].values 
+        x1_2_coords = x1_2_data[pc_cols].values 
+        x1_3_coords = x1_3_data[pc_cols].values
+        
+        x1_1_coords = x1_1_coords.astype(float)
+        x1_2_coords = x1_2_coords.astype(float)
+        x1_3_coords = x1_3_coords.astype(float)
+
+        # Target size is now the minimum across all three endpoint clusters
+        target_size = min(len(x1_1_coords), len(x1_2_coords), len(x1_3_coords))
+        
+        # Helper function to select points closest to centroid
+        def select_closest_to_centroid(coords, target_size):
+            if len(coords) <= target_size:
+                return coords
+            
+            # Calculate centroid
+            centroid = np.mean(coords, axis=0)
+            
+            # Calculate distances to centroid
+            distances = np.linalg.norm(coords - centroid, axis=1)
+            
+            # Get indices of closest points
+            closest_indices = np.argsort(distances)[:target_size]
+            
+            return coords[closest_indices]
+        
+        # Sample all endpoint clusters to target size using centroid-based selection
+        x1_1_coords = select_closest_to_centroid(x1_1_coords, target_size)
+        x1_2_coords = select_closest_to_centroid(x1_2_coords, target_size)
+        x1_3_coords = select_closest_to_centroid(x1_3_coords, target_size)
+        
+        dmso_cluster_counts = dmso_data[leiden_dmso_col].value_counts()
+        
+        # DMSO (unchanged)
+        largest_dmso_cluster = dmso_cluster_counts.index[0]
+        dmso_cluster_data = dmso_data[dmso_data[leiden_dmso_col] == largest_dmso_cluster]
+        
+        dmso_coords = dmso_cluster_data[pc_cols].values
+        
+        # Random sampling from largest DMSO cluster to match target size
+        # For DMSO, we'll also use centroid-based selection for consistency
+        if len(dmso_coords) >= target_size:
+            x0_coords = select_closest_to_centroid(dmso_coords, target_size)
+        else:
+            # If largest cluster is smaller than target, use all of it and pad with other DMSO cells
+            remaining_needed = target_size - len(dmso_coords)
+            other_dmso_data = dmso_data[dmso_data[leiden_dmso_col] != largest_dmso_cluster]
+            other_dmso_coords = other_dmso_data[pc_cols].values
+            
+            if len(other_dmso_coords) >= remaining_needed:
+                # Select closest to centroid from other DMSO cells
+                other_selected = select_closest_to_centroid(other_dmso_coords, remaining_needed)
+                x0_coords = np.vstack([dmso_coords, other_selected])
+            else:
+                # Use all available DMSO cells and reduce target size
+                all_dmso_coords = dmso_data[pc_cols].values
+                target_size = min(target_size, len(all_dmso_coords))
+                x0_coords = select_closest_to_centroid(all_dmso_coords, target_size)
+                
+                # Re-select endpoint clusters with updated target size
+                x1_1_coords = select_closest_to_centroid(x1_1_data[pc_cols].values.astype(float), target_size)
+                x1_2_coords = select_closest_to_centroid(x1_2_data[pc_cols].values.astype(float), target_size)
+                x1_3_coords = select_closest_to_centroid(x1_3_data[pc_cols].values.astype(float), target_size)
+        
+        # No need to resample since we already selected the right number
+        # The endpoint clusters are already at target_size from centroid-based selection
+        
+        self.n_samples = target_size
+        
+        # for plotting
+        self.coords_t0 = torch.tensor(x0_coords, dtype=torch.float32)
+        self.coords_t1_1 = torch.tensor(x1_1_coords, dtype=torch.float32)
+        self.coords_t1_2 = torch.tensor(x1_2_coords, dtype=torch.float32)
+        self.coords_t1_3 = torch.tensor(x1_3_coords, dtype=torch.float32)
+        
+        self.time_labels = np.concatenate([
+            np.zeros(len(self.coords_t0)),    # t=0
+            np.ones(len(self.coords_t1_1)),     # t=1
+            np.ones(len(self.coords_t1_2)),     # t=1
+            np.ones(len(self.coords_t1_3)),     # t=1
+        ])
+        
+        x0 = torch.tensor(x0_coords, dtype=torch.float32)
+        x1_1 = torch.tensor(x1_1_coords, dtype=torch.float32)
+        x1_2 = torch.tensor(x1_2_coords, dtype=torch.float32)
+        x1_3 = torch.tensor(x1_3_coords, dtype=torch.float32)
+        
+        split_index = int(target_size * self.split_ratios[0])
+        
+        if target_size - split_index < self.batch_size:
+            split_index = target_size - self.batch_size
+        
+        train_x0 = x0[:split_index]
+        val_x0 = x0[split_index:]
+        train_x1_1 = x1_1[:split_index]
+        val_x1_1 = x1_1[split_index:]
+        train_x1_2 = x1_2[:split_index]
+        val_x1_2 = x1_2[split_index:]
+        train_x1_3 = x1_3[:split_index]
+        val_x1_3 = x1_3[split_index:]
+        
+        self.val_x0 = val_x0
+        self.val_x1_1 = val_x1_1
+        self.val_x1_2 = val_x1_2
+        self.val_x1_3 = val_x1_3
+
+        train_x0_weights = torch.full((train_x0.shape[0], 1), fill_value=1.0)
+        train_x1_1_weights = torch.full((train_x1_1.shape[0], 1), fill_value=0.603)
+        train_x1_2_weights = torch.full((train_x1_2.shape[0], 1), fill_value=0.255)
+        train_x1_3_weights = torch.full((train_x1_3.shape[0], 1), fill_value=0.142)
+        
+        val_x0_weights = torch.full((val_x0.shape[0], 1), fill_value=1.0)
+        val_x1_1_weights = torch.full((val_x1_1.shape[0], 1), fill_value=0.603)
+        val_x1_2_weights = torch.full((val_x1_2.shape[0], 1), fill_value=0.255)
+        val_x1_3_weights = torch.full((val_x1_3.shape[0], 1), fill_value=0.142)
+        
+        # Updated train dataloaders to include x1_3
+        self.train_dataloaders = {
+            "x0": DataLoader(TensorDataset(train_x0, train_x0_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_1": DataLoader(TensorDataset(train_x1_1, train_x1_1_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(train_x1_2, train_x1_2_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_3": DataLoader(TensorDataset(train_x1_3, train_x1_3_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+        }
+        
+        # Updated val dataloaders to include x1_3
+        self.val_dataloaders = {
+            "x0": DataLoader(TensorDataset(val_x0, val_x0_weights), batch_size=self.batch_size, shuffle=False, drop_last=True),
+            "x1_1": DataLoader(TensorDataset(val_x1_1, val_x1_1_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(val_x1_2, val_x1_2_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+            "x1_3": DataLoader(TensorDataset(val_x1_3, val_x1_3_weights), batch_size=self.batch_size, shuffle=True, drop_last=True),
+        }
+        
+        all_coords = df[pc_cols].dropna().values.astype(float)
+        self.dataset = torch.tensor(all_coords, dtype=torch.float32)
+        self.tree = cKDTree(all_coords)
+
+        self.test_dataloaders = {
+            "x0": DataLoader(TensorDataset(val_x0, val_x0_weights), batch_size=self.val_x0.shape[0], shuffle=False, drop_last=False),
+            "x1_1": DataLoader(TensorDataset(val_x1_1, val_x1_1_weights), batch_size=self.val_x1_1.shape[0], shuffle=True, drop_last=True),
+            "x1_2": DataLoader(TensorDataset(val_x1_2, val_x1_2_weights), batch_size=self.val_x1_2.shape[0], shuffle=True, drop_last=True),
+            "x1_3": DataLoader(TensorDataset(val_x1_3, val_x1_3_weights), batch_size=self.val_x1_3.shape[0], shuffle=True, drop_last=True),
+            "dataset": DataLoader(TensorDataset(self.dataset), batch_size=self.dataset.shape[0], shuffle=False, drop_last=False),
+        }
+
+        # Updated metric samples - now using 4 clusters instead of 3
+        #km_all = KMeans(n_clusters=4, random_state=42).fit(self.dataset.numpy())
+        km_all = KMeans(n_clusters=4, random_state=0).fit(self.dataset[:, :3].numpy())
+
+        cluster_labels = km_all.labels_
+        
+        cluster_0_mask = cluster_labels == 0
+        cluster_1_mask = cluster_labels == 1
+        cluster_2_mask = cluster_labels == 2
+        cluster_3_mask = cluster_labels == 3
+        
+        samples = self.dataset.cpu().numpy()
+        
+        cluster_0_data = samples[cluster_0_mask]
+        cluster_1_data = samples[cluster_1_mask]
+        cluster_2_data = samples[cluster_2_mask]
+        cluster_3_data = samples[cluster_3_mask]
+                
+        self.metric_samples_dataloaders = [
+            DataLoader(
+                torch.tensor(cluster_1_data, dtype=torch.float32),
+                batch_size=cluster_1_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            DataLoader(
+                torch.tensor(cluster_3_data, dtype=torch.float32),
+                batch_size=cluster_3_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            
+            
+            DataLoader(
+                torch.tensor(cluster_2_data, dtype=torch.float32),
+                batch_size=cluster_2_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+            DataLoader(
+                torch.tensor(cluster_0_data, dtype=torch.float32),
+                batch_size=cluster_0_data.shape[0],
+                shuffle=False,
+                drop_last=False,
+            ),
+        ]
+        
+    def train_dataloader(self):
+        combined_loaders = {
+            "train_samples": CombinedLoader(self.train_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    def val_dataloader(self):
+        combined_loaders = {
+            "val_samples": CombinedLoader(self.val_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    
+    
+    def test_dataloader(self):
+        combined_loaders = {
+            "test_samples": CombinedLoader(self.test_dataloaders, mode="min_size"),
+            "metric_samples": CombinedLoader(
+                self.metric_samples_dataloaders, mode="min_size"
+            ),
+        }
+
+        return CombinedLoader(combined_loaders, mode="max_size_cycle")
+
+    def get_manifold_proj(self, points):
+        """Adapted for 2D cell data - uses local neighborhood averaging instead of plane fitting"""
+        return partial(self.local_smoothing_op, tree=self.tree, dataset=self.dataset)
+
+    @staticmethod
+    def local_smoothing_op(x, tree, dataset, k=10, temp=1e-3):
+        """
+        Apply local smoothing based on k-nearest neighbors in the full dataset
+        This replaces the plane projection for 2D manifold regularization
+        """
+        points_np = x.detach().cpu().numpy()
+        _, idx = tree.query(points_np, k=k)
+        nearest_pts = dataset[idx]  # Shape: (batch_size, k, 2)
+        
+        # Compute weighted average of neighbors
+        dists = (x.unsqueeze(1) - nearest_pts).pow(2).sum(-1, keepdim=True)
+        weights = torch.exp(-dists / temp)
+        weights = weights / weights.sum(dim=1, keepdim=True)
+        
+        # Weighted average of neighbors
+        smoothed = (weights * nearest_pts).sum(dim=1)
+        
+        # Blend original point with smoothed version
+        alpha = 0.3  # How much smoothing to apply
+        return (1 - alpha) * x + alpha * smoothed
+    
+    def get_timepoint_data(self):
+        """Return data organized by timepoints for visualization"""
+        return {
+            't0': self.coords_t0,
+            't1_1': self.coords_t1_1, 
+            't1_2': self.coords_t1_2, 
+            't1_3': self.coords_t1_3, 
+            'time_labels': self.time_labels
+        }
+    
+def get_datamodule():
+    datamodule = ThreeBranchTahoeDataModule(args)
+    datamodule.setup(stage="fit")   
+    return datamodule    

entangled-cell/entangledcell_module_three.py

@@ -0,0 +1,871 @@
+import os
+import sys
+os.environ["CUDA_VISIBLE_DEVICES"] = "5"
+
+import torch
+import wandb
+import matplotlib.pyplot as plt
+import pytorch_lightning as pl
+
+import numpy as np
+
+from torch.distributions import Normal
+from geo_metrics.metric_factory import natural_gradient_force
+import math
+from train_utils import make_aligned_clusters
+from matplotlib.colors import LinearSegmentedColormap
+from eval import compute_distribution_distances, compute_wasserstein_distances
+import json, time, csv
+
+
+class EntangledNetTrainBaseThree(pl.LightningModule):
+    def __init__(
+        self,
+        args,
+        bias_net, # input bias net
+        data_manifold_metric,
+        timepoint_data,
+        ot_sampler=None,
+        vel_conditioned=False,
+    ):
+        super().__init__()
+        self.args = args
+                
+        self.ot_sampler = ot_sampler
+        
+        self.bias_net = bias_net
+        
+        self.data_manifold_metric = data_manifold_metric
+        
+        self.target_measure = PathObjective(args)
+        if args.training:
+            self.replay = ReplayBuffer(args)
+        
+        self.dt = float(1.0 / args.num_steps)
+        self.std = (2.0 * args.kT / (args.friction * self.dt)) ** 0.5
+        self.log_prob = Normal(0, self.std).log_prob
+        self.timepoint_data = timepoint_data
+        self.vel_conditioned = vel_conditioned
+        self.dir_only = getattr(args, "dir_only", False)
+        #self.device = args.device
+        
+    # returns the bias force given the position, velocity and target
+    def forward(self, pos, vel, target):
+        # output velocity given branch_idx
+        if self.vel_conditioned:
+            # Use velocity direction (unit vector) instead of full velocity
+            if self.dir_only:
+                velocity_magnitude = torch.norm(vel, dim=-1, keepdim=True)
+                velocity_direction = vel / (velocity_magnitude + 1e-8)  # Avoid division by zero
+
+                return self.bias_net(pos, velocity_direction, target)
+            else:
+                return self.bias_net(pos, vel, target)
+
+        return self.bias_net(pos, target)
+    
+    def on_train_epoch_start(self):
+        pass
+    
+    def _sample(self, x0, x1, metric_samples):
+        """
+        Simulate first-order velocity dynamics 
+        
+        x0: initial positions of batch (B, N, g)
+        x1: final positions of batch (B, N, g)
+        """
+        device = x0.device
+        print(device)
+        
+        B, N, G = x0.shape
+        T = self.args.num_steps
+        
+        gamma = float(self.args.friction)
+        kT = float(getattr(self.args, "kT", 0.1))
+
+        positions = torch.empty((B, T+1, N, G), dtype=x0.dtype, device=device)
+        forces = torch.empty((B, T, N, G), dtype=x0.dtype, device=device)
+        biases = torch.empty((B, T, N, G), dtype=x0.dtype, device=device)
+
+        # set initial positions
+        positions[:, 0] = x0.clone()
+        pos = x0.clone()
+        
+        target_positions = x1.clone().to(device, dtype=x0.dtype) 
+        #target_positions = x1.clone().unsqueeze(dim=1).repeat(1, T+1, 1, 1)
+        
+        for t_idx in range(T):
+            if t_idx == 0:
+                velocity = torch.zeros_like(pos)
+            else:
+                velocity = (pos - positions[:, t_idx - 1]) / self.dt
+                
+            
+            F_nat, _ = natural_gradient_force(self.data_manifold_metric, 
+                                           pos,
+                                           metric_samples,
+                                           t_idx,
+                                           )
+            
+            base_force = F_nat # unbiased base force
+            # learned bias force
+            if self.vel_conditioned:
+                if self.dir_only:
+                    velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                    velocity_direction = velocity / (velocity_magnitude + 1e-8)  # Avoid division by zero
+                    
+                    bias_force = self.bias_net(pos.detach(), 
+                                            velocity_direction.detach(), 
+                                            target_positions.detach()).detach()
+                else:
+                    bias_force = self.bias_net(pos.detach(), 
+                                            velocity.detach(), 
+                                            target_positions.detach()).detach()
+            else:
+                bias_force = self.bias_net(pos.detach(), 
+                                           target_positions.detach()).detach()
+
+            if kT > 0:
+                xi = torch.randn_like(pos) * ((2.0 * kT * self.dt / gamma) ** 0.5)
+            else:
+                xi = 0.0
+            
+            pos = pos + (self.dt / gamma) * (base_force + bias_force) + xi
+            
+            positions[:, t_idx + 1] = pos.clone()
+            forces[:, t_idx] = base_force.clone()
+            biases[:, t_idx] = bias_force.clone()
+        
+        log_tpm, final_idx, log_ri = self.target_measure(positions, target_positions, forces)
+        
+        if self.args.training:
+            self.replay.add_ranked((positions.detach(), 
+                                    target_positions.detach(),
+                                    forces.detach(),
+                                    log_tpm.detach(),
+                                    log_ri.detach()))
+            
+        for i in range(B):
+            end = int(final_idx[i].item()) + 1 if torch.is_tensor(final_idx) else T + 1
+            np.save(f"{self.args.save_dir}/positions/{i}.npy", positions[i, :end].detach().cpu().numpy())
+        
+        return positions, target_positions, forces, log_tpm, log_ri
+        
+    def _compute_loss(self):
+        positions, target_positions, base_forces, log_tpm, log_ri = self.replay.sample()
+        # shapes: pos (B,T+1,N,G), tgt (B,N,G), base_forces (B,T,N,G)
+        
+        gamma = float(self.args.friction)
+
+        B, T, N, G = base_forces.shape
+        v = (positions[:, 1:] - positions[:, :-1]) / self.dt          # (B,T,N,G)
+
+        # rebuild bias per step for correct mean
+        x_t   = positions[:, :-1].reshape(-1, N, G)
+        v_t   = v.reshape(-1, N, G)  # reshape velocity to match other tensors
+        tgt_t = target_positions[:, None].expand(-1, T, N, G).reshape(-1, N, G)
+        if self.vel_conditioned:
+            if self.dir_only:
+                velocity_magnitude = torch.norm(v_t, dim=-1, keepdim=True)
+                velocity_direction = v_t / (velocity_magnitude + 1e-8)  # Avoid division by zero
+                B_t   = self.bias_net(x_t, velocity_direction, tgt_t).view(B, T, N, G)
+            else:
+                B_t   = self.bias_net(x_t, v_t, tgt_t).view(B, T, N, G)
+        else:
+            B_t   = self.bias_net(x_t, tgt_t).view(B, T, N, G)
+
+        means = (base_forces + B_t) / self.args.friction
+        resid = v - means
+
+        sigma_v = math.sqrt(2.0 * self.args.kT / (gamma * self.dt))
+        sigma_v = torch.as_tensor(sigma_v, dtype=resid.dtype, device=resid.device)
+        log_bpm = Normal(0.0, sigma_v).log_prob(resid).mean((1,2,3))
+
+        # control variate
+        cv = self.args.control_variate
+        if cv == "global":   
+            log_z = self.bias_net.log_z
+        elif cv == "local":  
+            log_z = (log_tpm - log_bpm).mean().detach()
+        elif cv == "zero":   
+            log_z = 0.0
+        else: raise ValueError(cv)
+
+        # objective
+        if self.args.objective == "ce":
+            log_rnd = (log_tpm - log_bpm.detach())
+            weights = torch.softmax(log_rnd, dim=0)
+            loss = -(weights * log_bpm).sum()
+            
+        else:  # 'lv'
+            loss = (log_z + log_bpm - log_tpm).pow(2).mean()
+
+        return loss, log_ri.mean()
+        
+    def training_step(self, batch, batch_idx):
+        epoch = self.current_epoch
+        
+        main_batch = batch[0]["train_samples"][0]
+        metric_batch = batch[0]["metric_samples"][0]
+        
+        x0s = main_batch["x0"][0]
+        x1s = main_batch["x1_1"][0] # train on cluster 1
+        N   = self.args.num_particles
+        
+        x0_clusters, x1_clusters, idx1 = \
+            make_aligned_clusters(self.ot_sampler, x0s, x1s, N, replace=True)
+        
+        sample_pairs = [
+            (metric_batch[0], metric_batch[1]),  # x0 → x1_1 (branch 1)
+        ]
+        
+        batch = self._sample(x0_clusters, x1_clusters, sample_pairs)
+        
+        
+        # timesteps from 0 to 1
+        self.timesteps = torch.linspace(0.0, 1.0, len(main_batch["x0"])).tolist()
+        loss, mean_log_ri = self._compute_loss()
+        
+        
+        self.log(
+            "train/loss",
+            loss,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        self.log(
+            "train/mean_log_ri",
+            mean_log_ri,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        
+        return loss
+
+    def validation_step(self, batch, batch_idx):
+        main_batch = batch[0]["val_samples"][0]
+        metric_batch = batch[0]["metric_samples"][0]
+        
+        x0s = main_batch["x0"][0]
+        x1s = main_batch["x1_2"][0] # validate on cluster 2
+        N   = self.args.num_particles
+        
+        x0_clusters, x1_clusters, idx1 = \
+            make_aligned_clusters(self.ot_sampler, x0s, x1s, N, replace=True)
+        
+        sample_pairs = [
+            (metric_batch[0], metric_batch[1]),  # x0 → x1_1 (branch 1)
+        ]
+        
+        batch = self._sample(x0_clusters, x1_clusters, sample_pairs)
+        
+        
+        # timesteps from 0 to 1
+        self.timesteps = torch.linspace(0.0, 1.0, len(main_batch["x0"])).tolist()
+        val_loss, mean_log_ri = self._compute_loss()
+        
+        
+        self.log(
+            "val/loss",
+            val_loss,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        self.log(
+            "val/mean_log_ri",
+            mean_log_ri,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        
+        return val_loss
+
+    def optimizer_step(self, *args, **kwargs):
+        super().optimizer_step(*args, **kwargs)
+        
+
+    def configure_optimizers(self):
+        exclude = {id(self.bias_net.log_z)}
+        params_except = [p for p in self.bias_net.parameters() if id(p) not in exclude]
+        optimizer = torch.optim.AdamW(
+            [
+                {"params": [self.bias_net.log_z], "lr": self.args.log_z_lr},
+                {"params": params_except, "lr": self.args.policy_lr},
+            ]
+        )
+
+        return optimizer
+
+class EntangledNetTrainCellThree(EntangledNetTrainBaseThree):
+    @torch.no_grad()
+    def plot_trajs(
+        self, traj, title, fname, targets,
+        timepoint_data=None, # dict with keys 't0','t1'
+        cmap=None, 
+        c_end='#B83CFF',
+        x_label="PC1", y_label="PC2",
+        save_dir=None,
+
+    ):
+        """
+        traj:  (B, T+1, N, 2)  torch tensor
+        targets: (B, N, 2)     torch tensor
+        timepoint_data (optional): {'t0': (M0,2), 't1': (M1,2)} np arrays or tensors
+        """
+                
+        custom_colors_1 = ["#05009E", "#A19EFF", "#D577FF"]
+        custom_colors_2 = ["#05009E", "#A19EFF", "#50B2D7"]
+        custom_cmap_1 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_1)
+        custom_cmap_2 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_2)
+        
+        # --- to numpy ---
+        tb = traj[..., :2].detach().cpu().numpy()        # (B,T+1,N,2)
+        targ2 = targets[..., :2].detach().cpu().numpy()  # (B,N,2)
+
+        # Optional background conversion
+        def _to_np(x):
+            if x is None: return None
+            return x.detach().cpu().numpy() if hasattr(x, "detach") else x
+        
+        def to_np_2d(x):
+            """Convert to np and force last dim=2 (take first two PCs). Returns None if <2 dims."""
+            if x is None:
+                return None
+            arr = x.detach().cpu().numpy() if hasattr(x, "detach") else np.asarray(x)
+            if arr.ndim == 1:  # (G,) -> (1,G)
+                arr = arr[None, :]
+            if arr.shape[-1] < 2:
+                return None
+            arr2 = arr[..., :2].reshape(-1, 2)
+            return arr2
+
+        t0_bg = to_np_2d(timepoint_data['t0']) if (timepoint_data and 't0' in timepoint_data) else None
+        t1_bg = to_np_2d(timepoint_data['t1']) if (timepoint_data and 't1' in timepoint_data) else None
+
+        if t0_bg is not None or t1_bg is not None:
+            coords_list = []
+            if t0_bg is not None: coords_list.append(t0_bg)
+            if t1_bg is not None: coords_list.append(t1_bg)
+            coords_list.append(tb.reshape(-1, 2))
+            coords_list.append(targ2.reshape(-1, 2))
+            all_coords = np.concatenate(coords_list, axis=0)
+            x_min, x_max = all_coords[:, 0].min(), all_coords[:, 0].max()
+            y_min, y_max = all_coords[:, 1].min(), all_coords[:, 1].max()
+            x_margin = 0.05 * max(1e-12, (x_max - x_min))
+            y_margin = 0.05 * max(1e-12, (y_max - y_min))
+            x_min -= x_margin; x_max += x_margin
+            y_min -= y_margin; y_max += y_margin
+        else:
+            x_min = y_min = -np.inf
+            x_max = y_max = +np.inf
+
+        # figure
+        fig, ax = plt.subplots(figsize=(10, 8))
+
+        # background timepoints
+        if t0_bg is not None:
+            ax.scatter(t0_bg[:, 0], t0_bg[:, 1],
+                    c='#05009E', s=80, alpha=0.4, marker='x',
+                    label='t=0 cells', linewidth=1.5)
+        if t1_bg is not None:
+            ax.scatter(t1_bg[:, 0], t1_bg[:, 1],
+                    c=c_end, s=80, alpha=0.4, marker='x',
+                    label='t=1 cells', linewidth=1.5)
+
+        # color map for temporal segments
+        if cmap is None:
+            cmap = custom_cmap_1
+        num_segments = tb.shape[1]  # T+1 points -> T segments, but use T+1 for colors indexing
+        colors = cmap(np.linspace(0, 1, max(2, num_segments)))
+
+        # trajectories as time-colored segments
+        B, T1, N, _ = tb.shape
+        for b in range(B):
+            for n in range(N):
+                xy = tb[b, :, n, :]  # (T+1, 2)
+                # segment plotting per time step
+                for t in range(T1 - 1):
+                    ax.plot(
+                        xy[t:t+2, 0], xy[t:t+2, 1],
+                        color=colors[t], linewidth=2, alpha=0.8, zorder=2
+                    )
+
+        # start/end dots with white edges
+        starts = tb[:, 0, :, :].reshape(-1, 2) 
+        ends   = tb[:, -1, :, :].reshape(-1, 2) 
+        ax.scatter(starts[:, 0], starts[:, 1],
+                c='#05009E', s=30, marker='o', label='Trajectory Start',
+                zorder=5, edgecolors='white', linewidth=1)
+        ax.scatter(ends[:, 0], ends[:, 1],
+                c=c_end, s=30, marker='o', label='Trajectory End',
+                zorder=5, edgecolors='white', linewidth=1)
+
+        tars = targ2.reshape(-1, 2)
+        ax.scatter(tars[:, 0], tars[:, 1],
+                s=24, marker='x', linewidths=1.5, c='#B83CFF',
+                alpha=0.7, label='targets', zorder=4)
+
+        if np.isfinite(x_min):
+            ax.set_xlim(x_min, x_max)
+            ax.set_ylim(y_min, y_max)
+        ax.set_xlabel(x_label, fontsize=12)
+        ax.set_ylabel(y_label, fontsize=12)
+        ax.set_title(title, fontsize=14)
+        ax.grid(True, alpha=0.3)
+        ax.legend(loc='upper right', fontsize=12, frameon=False)
+        ax.set_aspect('equal', adjustable='box')
+
+        plt.tight_layout()
+
+        if save_dir is None:
+            out_path = os.path.join(self.args.save_dir, "figures", self.args.data_name)
+            os.makedirs(out_path, exist_ok=True)
+        else:
+            out_path = save_dir
+            os.makedirs(out_path, exist_ok=True)
+
+        fpath = os.path.join(out_path, fname)
+        plt.savefig(fpath, dpi=300)
+        print(f"figure saved: {fpath}")
+        plt.close(fig)
+
+    def test_step(self, batch, batch_idx):
+        main_batch    = batch[0]["test_samples"][0]
+        x0s           = main_batch["x0"][0] # (B,G) or (B,N,G)
+        x1_1s         = main_batch["x1_1"][0] # training endpoint 
+        x1_2s         = main_batch["x1_2"][0] # unseen endpoint 1
+        x1_3s         = main_batch["x1_3"][0] # unseen endpoint 2
+        #x1s = torch.cat([x1_1s, x1_2s], dim=0)  # (M1+M2,G) or (B,G)
+        dataset_full  = main_batch["dataset"][0]   # (M,G)
+        
+        device = x0s.device
+
+        #B, N, G = x0s.shape
+        N    = self.args.num_particles
+        T    = self.args.num_steps
+        G    = self.args.dim
+        gamma = float(self.args.friction)
+        kT    = float(getattr(self.args, "kT", 0.1))
+        ell   = float(getattr(self.args, "adj_length_scale", 1.0))
+        noise_scale = (0.0 if kT <= 0 else math.sqrt(2.0 * kT * self.dt / gamma))
+
+        # Ensure pools are (M,G)
+        if x1_1s.ndim == 3: x1_1s = x1_1s.reshape(-1, G)
+        if x1_2s.ndim == 3: x1_2s = x1_2s.reshape(-1, G)
+        if x1_3s.ndim == 3: x1_3s = x1_3s.reshape(-1, G)
+
+        x0c_1, x1c_1, _ = make_aligned_clusters(self.ot_sampler, x0s, x1_1s, N, replace=True)   # to training endpoint
+        x0c_2, x1c_2, _ = make_aligned_clusters(self.ot_sampler, x0s, x1_2s, N, replace=True)   # to unseen endpoint
+        x0c_3, x1c_3, _ = make_aligned_clusters(self.ot_sampler, x0s, x1_3s, N, replace=True)   # to unseen endpoint
+
+        B = x0c_1.shape[0]
+        
+        # rollout base-only dynamics (no bias)
+        def rollout_base(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+                
+                F_nat, _ = natural_gradient_force(
+                    self.data_manifold_metric, pos, metric_samples=None, timestep=t
+                )                                             # (B,N,G)
+                base_force = F_nat
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * base_force + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+        # rollout bias-only (use bias for dynamics; base only to condition the net)
+        def rollout_bias_only(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+                if t == 0: 
+                    velocity = torch.zeros_like(pos)
+                else:
+                    velocity = (pos - traj[:, t-1]) / self.dt
+
+                if self.vel_conditioned:
+                    if self.dir_only:
+                        velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                        velocity_direction = velocity / (velocity_magnitude + 1e-8)
+                        
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity_direction.detach(), x1c.detach()
+                        ).detach()
+                    else:
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity.detach(), x1c.detach()
+                        ).detach()
+                else:
+                    bias_force = self.bias_net(
+                        pos.detach(), x1c.detach()
+                    ).detach()                                    # (B,N,G)
+                    
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * (bias_force) + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+        # rollout bias+base (controlled dynamics)
+        def rollout_bias_plus_base(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+                if t == 0: 
+                    velocity = torch.zeros_like(pos)
+                else:
+                    velocity = (pos - traj[:, t-1]) / self.dt
+
+                F_nat, _ = natural_gradient_force(
+                    self.data_manifold_metric, pos, metric_samples=None, timestep=t
+                )                                             # (B,N,G)
+                base_force =  F_nat
+                
+                if self.vel_conditioned:
+                    if self.dir_only:
+                        velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                        velocity_direction = velocity / (velocity_magnitude + 1e-8)
+                        
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity_direction.detach(), x1c.detach()
+                        ).detach()
+                    else:
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity.detach(), x1c.detach()
+                        ).detach()
+                else:
+                    bias_force = self.bias_net(
+                        pos.detach(), x1c.detach()
+                    ).detach()
+                    
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * (base_force + bias_force) + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+
+        traj_to_x1_1 = rollout_base(x0c_1, x1c_1)
+        traj_to_x1_2 = rollout_base(x0c_2, x1c_2)
+        traj_to_x1_3 = rollout_base(x0c_3, x1c_3)
+
+        traj_bias_only_x1_1   = rollout_bias_only(x0c_1, x1c_1)
+        traj_bias_plus_x1_1   = rollout_bias_plus_base(x0c_1, x1c_1)
+        traj_bias_only_x1_2   = rollout_bias_only(x0c_2, x1c_2)
+        traj_bias_plus_x1_2   = rollout_bias_plus_base(x0c_2, x1c_2)
+        traj_bias_only_x1_3   = rollout_bias_only(x0c_3, x1c_3)
+        traj_bias_plus_x1_3   = rollout_bias_plus_base(x0c_3, x1c_3)
+
+        # plot (first two dims)
+        save_dir = os.path.join(self.args.save_dir, "figures", self.args.data_name)
+        os.makedirs(save_dir, exist_ok=True)
+
+        ds2 = (dataset_full[:, :2].detach().cpu().numpy()
+               if isinstance(dataset_full, torch.Tensor) else dataset_full[:, :2])
+            
+        custom_colors_1 = ["#05009E", "#A19EFF", "#6B67EE"]
+        custom_colors_2 = ["#05009E", "#A19EFF", "#50B2D7"]
+        custom_colors_3 = ["#05009E", "#A19EFF", "#EABBFF"]
+        custom_cmap_1 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_1)
+        custom_cmap_2 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_2)
+        custom_cmap_3 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_3)
+        
+        t0_data = self.timepoint_data["t0"]
+        t1_data = torch.cat([self.timepoint_data["t1_1"], self.timepoint_data["t1_2"], self.timepoint_data["t1_3"]], 
+                            dim=0)
+        
+        # seen endpoint
+        self.plot_trajs(
+            traj_bias_only_x1_1,
+            "Bias-only → training endpoint (x1_1)",
+            f"{self.args.data_name}_bias_only_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_to_x1_1,
+            "Base-only trajectories → training endpoint (x1_1)",
+            f"{self.args.data_name}_base_only_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+        
+        self.plot_trajs(traj_bias_plus_x1_1,
+            "Bias + base trajectories → training endpoint (x1_1)",
+            f"{self.args.data_name}_bias_plus_base_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+
+        # unseen endpoint
+        self.plot_trajs(traj_to_x1_2,
+            "Base-only trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_base_only_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_only_x1_2,
+            "Bias-only trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_bias_only_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_plus_x1_2,
+            "Bias + base trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_bias_plus_base_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+
+        # unseen endpoint 3
+        self.plot_trajs(traj_to_x1_3,
+            "Base-only trajectories → unseen endpoint (x1_3)",
+            f"{self.args.data_name}_base_only_to_x1_3.png",
+            x1c_3,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_3,
+            c_end='#B83CFF',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_only_x1_3,
+            "Bias-only trajectories → unseen endpoint (x1_3)",
+            f"{self.args.data_name}_bias_only_to_x1_3.png",
+            x1c_3,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_3,
+            c_end='#B83CFF',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_plus_x1_3,
+            "Bias + base trajectories → unseen endpoint (x1_3)",
+            f"{self.args.data_name}_bias_plus_base_to_x1_3.png",
+            x1c_3,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_3,
+            c_end='#B83CFF',
+            save_dir=save_dir
+        )
+        
+        # quantitative metrics (per-cluster)
+        def eval_cluster_set(traj_B_T1_N_G, targets_B_N_G, tag: str):
+            finals = traj_B_T1_N_G[:, -1]          # (B, N, G)
+            B = finals.shape[0]
+
+            # accumulate per-anchor metrics, then mean over B
+            per_b_vals = []
+            for b in range(B):
+                pred_b = finals[b].to(device)         # (N, G)
+                true_b = targets_B_N_G[b].to(device)  # (N, G)
+                
+                names, vals = compute_distribution_distances(pred_b, true_b)
+                per_b_vals.append(vals)
+
+            per_b_vals = np.asarray(per_b_vals, dtype=float)   # (B, num_metrics)
+            mean_vals   = per_b_vals.mean(axis=0)
+            std_vals    = per_b_vals.std(axis=0, ddof=1) if B > 1 else np.zeros_like(mean_vals)
+
+            # log (Lightning-friendly); also return a dict
+            out = {}
+            for n, m, s in zip(names, mean_vals, std_vals):
+                self.log(f"test/{tag}/{n}",  float(m), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                self.log(f"test/{tag}/{n}_std", float(s), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                out[f"{n}"] = float(m)
+                out[f"{n}_std"] = float(s)
+            return out
+
+        # quantitative metrics (vs full distribution)
+        def eval_vs_full_distribution(traj_B_T1_N_G, full_target_distribution, tag: str):
+            finals = traj_B_T1_N_G[:, -1]          # (B, N, G)
+            
+            # flatten all trajectory endpoints into single distribution
+            pred_all = finals.reshape(-1, G).to(device)  # (B*N, G)
+            true_all = full_target_distribution.to(device)  # (M, G)
+            
+            pred_all = pred_all.float()
+            true_all = true_all.float()
+            
+            names, vals = compute_wasserstein_distances(pred_all, true_all)
+            
+            out = {}
+            for n, v in zip(names, vals):
+                self.log(f"test/{tag}/{n}", float(v), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                out[f"{n}"] = float(v)
+            return out
+
+        # quantitative metrics over multiple independent simulations
+        num_sims = 5
+        base_seed = 12345
+
+        def run_one_sim(sim_idx: int):
+            # re-rollout all six variants with a distinct RNG state
+            devices = [device.index] if device.type == "cuda" and device.index is not None else None
+            with torch.random.fork_rng(devices=devices):
+                
+                torch.manual_seed(base_seed + sim_idx)
+
+                tr_base_11 = rollout_base(x0c_1, x1c_1)
+                tr_base_12 = rollout_base(x0c_2, x1c_2)
+                tr_base_13 = rollout_base(x0c_3, x1c_3)
+
+                tr_bias_only_11 = rollout_bias_only(x0c_1, x1c_1)
+                tr_bias_plus_11 = rollout_bias_plus_base(x0c_1, x1c_1)
+
+                tr_bias_only_12 = rollout_bias_only(x0c_2, x1c_2)
+                tr_bias_plus_12 = rollout_bias_plus_base(x0c_2, x1c_2)
+
+                tr_bias_only_13 = rollout_bias_only(x0c_3, x1c_3)
+                tr_bias_plus_13 = rollout_bias_plus_base(x0c_3, x1c_3)
+
+            # evaluate per-cluster metrics (against clustered targets)
+            metrics = {}
+            metrics.update({f"base_x1_1/{k}": v for k, v in eval_cluster_set(tr_base_11,      x1c_1, "base/x1_1").items()})
+            metrics.update({f"base_x1_2/{k}": v for k, v in eval_cluster_set(tr_base_12,      x1c_2, "base/x1_2").items()})
+            metrics.update({f"base_x1_3/{k}": v for k, v in eval_cluster_set(tr_base_13,      x1c_3, "base/x1_3").items()})
+            metrics.update({f"bias_only_x1_1/{k}": v for k, v in eval_cluster_set(tr_bias_only_11, x1c_1, "bias_only/x1_1").items()})
+            metrics.update({f"bias_plus_x1_1/{k}": v for k, v in eval_cluster_set(tr_bias_plus_11, x1c_1, "bias_plus/x1_1").items()})
+            metrics.update({f"bias_only_x1_2/{k}": v for k, v in eval_cluster_set(tr_bias_only_12, x1c_2, "bias_only/x1_2").items()})
+            metrics.update({f"bias_plus_x1_2/{k}": v for k, v in eval_cluster_set(tr_bias_plus_12, x1c_2, "bias_plus/x1_2").items()})
+            metrics.update({f"bias_only_x1_3/{k}": v for k, v in eval_cluster_set(tr_bias_only_13, x1c_3, "bias_only/x1_3").items()})
+            metrics.update({f"bias_plus_x1_3/{k}": v for k, v in eval_cluster_set(tr_bias_plus_13, x1c_3, "bias_plus/x1_3").items()})
+            
+            # evaluate against full distributions
+            metrics.update({f"base_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_base_11, x1_1s, "base_vs_full/x1_1").items()})
+            metrics.update({f"base_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_base_12, x1_2s, "base_vs_full/x1_2").items()})
+            metrics.update({f"base_vs_full_x1_3/{k}": v for k, v in eval_vs_full_distribution(tr_base_13, x1_3s, "base_vs_full/x1_3").items()})
+            metrics.update({f"bias_only_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_bias_only_11, x1_1s, "bias_only_vs_full/x1_1").items()})
+            metrics.update({f"bias_plus_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_bias_plus_11, x1_1s, "bias_plus_vs_full/x1_1").items()})
+            metrics.update({f"bias_only_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_bias_only_12, x1_2s, "bias_only_vs_full/x1_2").items()})
+            metrics.update({f"bias_plus_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_bias_plus_12, x1_2s, "bias_plus_vs_full/x1_2").items()})
+            metrics.update({f"bias_only_vs_full_x1_3/{k}": v for k, v in eval_vs_full_distribution(tr_bias_only_13, x1_3s, "bias_only_vs_full/x1_3").items()})
+            metrics.update({f"bias_plus_vs_full_x1_3/{k}": v for k, v in eval_vs_full_distribution(tr_bias_plus_13, x1_3s, "bias_plus_vs_full/x1_3").items()})
+            
+            return metrics
+
+        # run K sims and collect metrics per run
+        metrics_runs = [run_one_sim(k) for k in range(num_sims)]
+
+        agg = {}
+        all_keys = sorted(metrics_runs[0].keys())
+
+        for key in all_keys:
+            vals = torch.tensor([m[key] for m in metrics_runs], dtype=torch.float32)
+            agg[f"{key}_runs_mean"] = vals.mean().item()
+            agg[f"{key}_runs_std"]  = (vals.std(unbiased=True).item() if num_sims > 1 else 0.0)
+
+            # Log for Lightning
+            self.log(f"test/{key}_runs_mean", agg[f"{key}_runs_mean"], on_step=False, on_epoch=True, logger=True)
+            self.log(f"test/{key}_runs_std",  agg[f"{key}_runs_std"],  on_step=False, on_epoch=True, logger=True)
+
+        if getattr(self.trainer, "is_global_zero", True):
+            out_dir = os.path.join(self.args.save_dir, "metrics", self.args.data_name)
+            os.makedirs(out_dir, exist_ok=True)
+            stamp = time.strftime("%Y%m%d-%H%M%S")
+            with open(os.path.join(out_dir, f"test_metrics_aggregated_{num_sims}runs_{stamp}.json"), "w") as f:
+                json.dump(agg, f, indent=2)
+        
+        return {"num_traj": B}
+            
+class ReplayBuffer:
+    def __init__(self, args):
+        BZ, T, N, G = args.buffer_size, args.num_steps, args.num_particles, args.dim
+        self.positions        = torch.zeros((BZ, T+1, N, G), device=args.device)
+        self.target_positions = torch.zeros((BZ, N,   G), device=args.device)
+        self.forces           = torch.zeros((BZ, T,   N, G), device=args.device)
+        self.log_tpm          = torch.zeros((BZ,), device=args.device)
+        self.rewards          = torch.zeros((BZ,), device=args.device)
+        self.batch_size, self.buffer_size, self.count = args.batch_size, args.buffer_size, 0
+
+    def add_ranked(self, data):
+        positions, target_positions, forces, log_tpm, rewards = data
+        # concat existing + new, keep top by reward
+        if self.count > 0:
+            pos = torch.cat([self.positions[:self.count], positions], dim=0)
+            tgt = torch.cat([self.target_positions[:self.count], target_positions], dim=0)
+            frc = torch.cat([self.forces[:self.count], forces], dim=0)
+            ltp = torch.cat([self.log_tpm[:self.count], log_tpm], dim=0)
+            rwd = torch.cat([self.rewards[:self.count], rewards], dim=0)
+        else:
+            pos, tgt, frc, ltp, rwd = positions, target_positions, forces, log_tpm, rewards
+        k = min(self.buffer_size, pos.size(0))
+        top_vals, top_idx = torch.topk(rwd, k=k, largest=True, sorted=False)
+        self.positions[:k]        = pos.index_select(0, top_idx)
+        self.target_positions[:k] = tgt.index_select(0, top_idx)
+        self.forces[:k]           = frc.index_select(0, top_idx)
+        self.log_tpm[:k]          = ltp.index_select(0, top_idx)
+        self.rewards[:k]          = top_vals
+        self.count = k
+
+    def sample(self):
+        assert self.count > 0, "buffer is empty"
+        idx = torch.randint(0, self.count, (self.batch_size,), device=self.positions.device)
+        return (
+            self.positions[idx], self.target_positions[idx],
+            self.forces[idx], self.log_tpm[idx], self.rewards[idx],
+        )
+    
+class PathObjective:
+    def __init__(self, args):
+        self.dt = float(1.0 / args.num_steps)
+        self.gamma = args.friction
+        self.kT = getattr(args, "kT", 0.1)
+        self.sigma_v = math.sqrt(2.0 * self.kT / (self.gamma * self.dt))
+        self.log_prob = Normal(0.0, self.sigma_v).log_prob
+        self.sigma = args.sigma
+        
+    def __call__(self, positions, target_positions, base_forces):
+        log_upm = self.unbiased_path_measure(positions, base_forces)
+        log_ri, final_idx = self.relaxed_indicator(positions, target_positions)
+        return log_upm + log_ri, final_idx, log_ri
+
+    def unbiased_path_measure(self, positions, base_forces):
+        v = (positions[:, 1:] - positions[:, :-1]) / self.dt
+        
+        means = base_forces / self.gamma # (B,T,N,G)
+        resid = v - means
+        return self.log_prob(resid).mean((1,2,3))
+
+    def relaxed_indicator(self, positions, target_positions):
+        # allow (B,N,G) or (B,T+1,N,G)
+        device = positions.device
+        if target_positions.ndim == 3:
+            target_positions = target_positions[:, None].expand_as(positions)
+            
+        target_positions = target_positions.to(device)
+        dist2  = (positions - target_positions).pow(2).mean((-2,-1)) # (B,T+1)
+        log_ri = -0.5 * dist2 / (self.sigma**2)
+        vals, idx = log_ri.max(dim=1)
+        return vals, idx

entangled-cell/entangledcell_module_unseen.py

@@ -0,0 +1,817 @@
+import os
+import sys
+os.environ["CUDA_VISIBLE_DEVICES"] = "5"
+
+import torch
+import wandb
+import matplotlib.pyplot as plt
+import pytorch_lightning as pl
+
+import numpy as np
+
+from torch.distributions import Normal
+from geo_metrics.metric_factory import natural_gradient_force
+import math
+from train_utils import make_aligned_clusters
+from matplotlib.colors import LinearSegmentedColormap
+from eval import compute_distribution_distances, compute_wasserstein_distances
+import json, time, csv
+
+
+class EntangledNetTrainBaseUnseen(pl.LightningModule):
+    def __init__(
+        self,
+        args,
+        bias_net, # input bias net
+        data_manifold_metric,
+        timepoint_data,
+        ot_sampler=None,
+        vel_conditioned=False,
+    ):
+        super().__init__()
+        self.args = args
+                
+        self.ot_sampler = ot_sampler
+        
+        self.bias_net = bias_net
+        
+        self.data_manifold_metric = data_manifold_metric
+        
+        self.target_measure = PathObjective(args)
+        if args.training:
+            self.replay = ReplayBuffer(args)
+        
+        self.dt = float(1.0 / args.num_steps)
+        self.std = (2.0 * args.kT / (args.friction * self.dt)) ** 0.5
+        self.log_prob = Normal(0, self.std).log_prob
+        self.timepoint_data = timepoint_data
+        self.vel_conditioned = vel_conditioned
+        self.dir_only = getattr(args, "dir_only", False)
+        #self.device = args.device
+        
+    # returns the bias force given the position, velocity and target
+    def forward(self, pos, vel, target):
+        if self.vel_conditioned:
+            if self.dir_only:
+                velocity_magnitude = torch.norm(vel, dim=-1, keepdim=True)
+                velocity_direction = vel / (velocity_magnitude + 1e-8)
+                return self.bias_net(pos, velocity_direction, target)
+            else:
+                return self.bias_net(pos, vel, target)
+
+        return self.bias_net(pos, target)
+
+    def on_train_epoch_start(self):
+        pass
+    
+    def _sample(self, x0, x1, metric_samples):
+        """
+        Simulate first-order velocity dynamics 
+        
+        x0: initial positions of batch (B, N, g)
+        x1: final positions of batch (B, N, g)
+        """
+        device = x0.device
+        print(device)
+        
+        B, N, G = x0.shape
+        T = self.args.num_steps
+        
+        gamma = float(self.args.friction)
+        kT = float(getattr(self.args, "kT", 0.0))
+
+        positions = torch.empty((B, T+1, N, G), dtype=x0.dtype, device=device)
+        forces = torch.empty((B, T, N, G), dtype=x0.dtype, device=device)
+        biases = torch.empty((B, T, N, G), dtype=x0.dtype, device=device)
+
+        # set initial positions
+        positions[:, 0] = x0
+        pos = x0.clone()
+        
+        target_positions = x1.clone().to(device, dtype=x0.dtype) 
+        #target_positions = x1.clone().unsqueeze(dim=1).repeat(1, T+1, 1, 1)
+        
+        for t_idx in range(T):
+            if t_idx == 0: 
+                velocity = torch.zeros_like(pos)
+            else:
+                velocity = (pos - positions[:, t_idx-1]) / self.dt
+                
+            
+            F_nat, _ = natural_gradient_force(self.data_manifold_metric, 
+                                           pos,
+                                           metric_samples,
+                                           t_idx,
+                                           )
+            
+            base_force =  F_nat # unbiased base force
+            # learned bias force
+            if self.vel_conditioned:
+                if self.dir_only:
+                    velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                    velocity_direction = velocity / (velocity_magnitude + 1e-8)  # Avoid division by zero
+                    
+                    bias_force = self.bias_net(pos.detach(), 
+                                            velocity_direction.detach(), 
+                                            target_positions.detach()).detach()
+                else:
+                    bias_force = self.bias_net(pos.detach(), 
+                                            velocity.detach(), 
+                                            target_positions.detach()).detach()
+            else:
+                bias_force = self.bias_net(pos.detach(), 
+                                           target_positions.detach()).detach()
+
+            if kT > 0:
+                xi = torch.randn_like(pos) * ((2.0 * kT * self.dt / gamma) ** 0.5)
+            else:
+                xi = 0.0
+            
+            pos = pos + (self.dt / gamma) * (base_force + bias_force) + xi
+            
+            positions[:, t_idx + 1] = pos.clone()
+            forces[:, t_idx] = base_force.clone()
+            biases[:, t_idx] = bias_force.clone()
+        
+        log_tpm, final_idx, log_ri = self.target_measure(positions, target_positions, forces)
+        
+        if self.args.training:
+            self.replay.add_ranked((positions.detach(), 
+                                    target_positions.detach(),
+                                    forces.detach(),
+                                    log_tpm.detach(),
+                                    log_ri.detach()))
+            
+        for i in range(B):
+            end = int(final_idx[i].item()) + 1 if torch.is_tensor(final_idx) else T + 1
+            np.save(f"{self.args.save_dir}/positions/{i}.npy", positions[i, :end].detach().cpu().numpy())
+        
+        return positions, target_positions, forces, log_tpm, log_ri
+        
+    def _compute_loss(self):
+        positions, target_positions, base_forces, log_tpm, log_ri = self.replay.sample()
+        # shapes: pos (B,T+1,N,G), tgt (B,N,G), base_forces (B,T,N,G)
+        
+        gamma = float(self.args.friction)
+
+        B, T, N, G = base_forces.shape
+        v = (positions[:, 1:] - positions[:, :-1]) / self.dt          # (B,T,N,G)
+
+        # rebuild bias per step for correct mean
+        x_t = positions[:, :-1].reshape(-1, N, G)
+        v_t = v.reshape(-1, N, G)  # reshape velocity to match other tensors
+        tgt_t = target_positions[:, None].expand(-1, T, N, G).reshape(-1, N, G)
+        
+        if self.vel_conditioned:
+            if self.dir_only:
+                velocity_magnitude = torch.norm(v_t, dim=-1, keepdim=True)
+                velocity_direction = v_t / (velocity_magnitude + 1e-8)
+                B_t = self.bias_net(x_t, velocity_direction, tgt_t).view(B, T, N, G)
+            else:
+                B_t = self.bias_net(x_t, v_t, tgt_t).view(B, T, N, G)
+        else:
+            B_t = self.bias_net(x_t, tgt_t).view(B, T, N, G)
+
+        means = (base_forces + B_t) / self.args.friction
+        resid = v - means
+
+        sigma_v = math.sqrt(2.0 * self.args.kT / (gamma * self.dt))
+        sigma_v = torch.as_tensor(sigma_v, dtype=resid.dtype, device=resid.device)
+        log_bpm = Normal(0.0, sigma_v).log_prob(resid).mean((1,2,3))
+
+        # control variate
+        cv = self.args.control_variate
+        if cv == "global":   
+            log_z = self.bias_net.log_z
+        elif cv == "local":  
+            log_z = (log_tpm - log_bpm).mean().detach()
+        elif cv == "zero":   
+            log_z = 0.0
+        else: raise ValueError(cv)
+
+        # ce objective
+        if self.args.objective == "ce":
+            log_rnd = (log_tpm - log_bpm.detach())
+            weights = torch.softmax(log_rnd, dim=0)
+            loss = -(weights * log_bpm).sum()
+            
+        else:  # lv loss
+            loss = (log_z + log_bpm - log_tpm).pow(2).mean()
+
+        return loss, log_ri.mean()
+        
+    def training_step(self, batch, batch_idx):
+        epoch = self.current_epoch
+        
+        main_batch = batch[0]["train_samples"][0]
+        metric_batch = batch[0]["metric_samples"][0]
+        
+        x0s = main_batch["x0"][0]
+        x1s = main_batch["x1_1"][0] # train on cluster 1
+        N   = self.args.num_particles
+        
+        x0_clusters, x1_clusters, idx1 = \
+            make_aligned_clusters(self.ot_sampler, x0s, x1s, N, replace=True)
+        
+        sample_pairs = [
+            (metric_batch[0], metric_batch[1]),  # x0 → x1_1 (branch 1)
+        ]
+        
+        batch = self._sample(x0_clusters, x1_clusters, sample_pairs)
+        
+        # timesteps from 0 to 1
+        self.timesteps = torch.linspace(0.0, 1.0, len(main_batch["x0"])).tolist()
+        loss, mean_log_ri = self._compute_loss()
+        
+        self.log(
+            "train/loss",
+            loss,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        self.log(
+            "train/mean_log_ri",
+            mean_log_ri,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        
+        return loss
+
+    def validation_step(self, batch, batch_idx):
+        main_batch = batch[0]["val_samples"][0]
+        metric_batch = batch[0]["metric_samples"][0]
+        
+        x0s = main_batch["x0"][0]
+        x1s = main_batch["x1_2"][0] # validate on cluster 2
+        N   = self.args.num_particles
+        
+        x0_clusters, x1_clusters, idx1 = \
+            make_aligned_clusters(self.ot_sampler, x0s, x1s, N, replace=True)
+        
+        sample_pairs = [
+            (metric_batch[0], metric_batch[1]),  # x0 -> x1_1 (branch 1)
+        ]
+        
+        batch = self._sample(x0_clusters, x1_clusters, sample_pairs)
+        
+        
+        # timesteps from 0 to 1
+        self.timesteps = torch.linspace(0.0, 1.0, len(main_batch["x0"])).tolist()
+        val_loss, mean_log_ri = self._compute_loss()
+        
+        
+        self.log(
+            "val/loss",
+            val_loss,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        self.log(
+            "val/mean_log_ri",
+            mean_log_ri,
+            on_step=False,
+            on_epoch=True,
+            prog_bar=True,
+            logger=True,
+        )
+        
+        return val_loss
+
+    def optimizer_step(self, *args, **kwargs):
+        super().optimizer_step(*args, **kwargs)
+        
+
+    def configure_optimizers(self):
+        exclude = {id(self.bias_net.log_z)}
+        params_except = [p for p in self.bias_net.parameters() if id(p) not in exclude]
+        optimizer = torch.optim.AdamW(
+            [
+                {"params": [self.bias_net.log_z], "lr": self.args.log_z_lr},
+                {"params": params_except, "lr": self.args.policy_lr},
+            ]
+        )
+
+        return optimizer
+
+class EntangledNetTrainCellUnseen(EntangledNetTrainBaseUnseen):
+    @torch.no_grad()
+    def plot_trajs(
+        self, traj, title, fname, targets,
+        timepoint_data=None, # dict with keys 't0','t1'
+        cmap=None, 
+        c_end='#B83CFF',
+        x_label="PC1", y_label="PC2",
+        save_dir=None,
+
+    ):
+                
+        custom_colors_1 = ["#05009E", "#A19EFF", "#D577FF"]
+        custom_colors_2 = ["#05009E", "#A19EFF", "#50B2D7"]
+        custom_cmap_1 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_1)
+        custom_cmap_2 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_2)
+        
+        tb = traj[..., :2].detach().cpu().numpy() # (B,T+1,N,2)
+        targ2 = targets[..., :2].detach().cpu().numpy() # (B,N,2)
+
+        # optional background conversion
+        def _to_np(x):
+            if x is None: return None
+            return x.detach().cpu().numpy() if hasattr(x, "detach") else x
+        
+        def to_np_2d(x):
+            """Convert to np and force last dim=2 (take first two PCs). Returns None if <2 dims."""
+            if x is None:
+                return None
+            arr = x.detach().cpu().numpy() if hasattr(x, "detach") else np.asarray(x)
+            if arr.ndim == 1:  # (G,) -> (1,G)
+                arr = arr[None, :]
+            if arr.shape[-1] < 2:
+                return None
+            arr2 = arr[..., :2].reshape(-1, 2)
+            return arr2
+
+        t0_bg = to_np_2d(timepoint_data['t0']) if (timepoint_data and 't0' in timepoint_data) else None
+        t1_bg = to_np_2d(timepoint_data['t1']) if (timepoint_data and 't1' in timepoint_data) else None
+
+        # axis limits (match global-limits logic with small margins if background present)
+        if t0_bg is not None or t1_bg is not None:
+            coords_list = []
+            if t0_bg is not None: coords_list.append(t0_bg)
+            if t1_bg is not None: coords_list.append(t1_bg)
+            coords_list.append(tb.reshape(-1, 2))
+            coords_list.append(targ2.reshape(-1, 2))
+            all_coords = np.concatenate(coords_list, axis=0)
+            x_min, x_max = all_coords[:, 0].min(), all_coords[:, 0].max()
+            y_min, y_max = all_coords[:, 1].min(), all_coords[:, 1].max()
+            x_margin = 0.05 * max(1e-12, (x_max - x_min))
+            y_margin = 0.05 * max(1e-12, (y_max - y_min))
+            x_min -= x_margin; x_max += x_margin
+            y_min -= y_margin; y_max += y_margin
+        else:
+            x_min = y_min = -np.inf
+            x_max = y_max = +np.inf
+
+        # figure
+        fig, ax = plt.subplots(figsize=(10, 8))
+
+        # background timepoints
+        if t0_bg is not None:
+            ax.scatter(t0_bg[:, 0], t0_bg[:, 1],
+                    c='#05009E', s=80, alpha=0.4, marker='x',
+                    label='t=0 cells', linewidth=1.5)
+        if t1_bg is not None:
+            ax.scatter(t1_bg[:, 0], t1_bg[:, 1],
+                    c=c_end, s=80, alpha=0.4, marker='x',
+                    label='t=1 cells', linewidth=1.5)
+
+        # color map for temporal segments
+        if cmap is None:
+            cmap = custom_cmap_1
+        num_segments = tb.shape[1]  # T+1 points -> T segments, but use T+1 for colors indexing
+        colors = cmap(np.linspace(0, 1, max(2, num_segments)))
+
+        B, T1, N, _ = tb.shape
+        for b in range(B):
+            for n in range(N):
+                xy = tb[b, :, n, :]  # (T+1, 2)
+                for t in range(T1 - 1):
+                    ax.plot(
+                        xy[t:t+2, 0], xy[t:t+2, 1],
+                        color=colors[t], linewidth=2, alpha=0.8, zorder=2
+                    )
+
+        starts = tb[:, 0, :, :].reshape(-1, 2)     # (B*N, 2)
+        ends   = tb[:, -1, :, :].reshape(-1, 2)    # (B*N, 2)
+        ax.scatter(starts[:, 0], starts[:, 1],
+                c='#05009E', s=30, marker='o', label='Trajectory Start',
+                zorder=5, edgecolors='white', linewidth=1)
+        ax.scatter(ends[:, 0], ends[:, 1],
+                c=c_end, s=30, marker='o', label='Trajectory End',
+                zorder=5, edgecolors='white', linewidth=1)
+        
+        tars = targ2.reshape(-1, 2)
+        ax.scatter(tars[:, 0], tars[:, 1],
+                s=24, marker='x', linewidths=1.5, c='#B83CFF',
+                alpha=0.7, label='targets', zorder=4)
+
+        if np.isfinite(x_min):
+            ax.set_xlim(x_min, x_max)
+            ax.set_ylim(y_min, y_max)
+        ax.set_xlabel(x_label, fontsize=12)
+        ax.set_ylabel(y_label, fontsize=12)
+        ax.set_title(title, fontsize=14)
+        ax.grid(True, alpha=0.3)
+        ax.legend(loc='upper right', fontsize=12, frameon=False)
+        ax.set_aspect('equal', adjustable='box')
+
+        plt.tight_layout()
+
+        if save_dir is None:
+            out_path = os.path.join(self.args.save_dir, "figures", self.args.data_name)
+            os.makedirs(out_path, exist_ok=True)
+        else:
+            out_path = save_dir
+            os.makedirs(out_path, exist_ok=True)
+
+        fpath = os.path.join(out_path, fname)
+        plt.savefig(fpath, dpi=300)
+        print(f"figure saved: {fpath}")
+        plt.close(fig)
+
+    def test_step(self, batch, batch_idx):
+        main_batch = batch[0]["test_samples"][0]
+        x0s = main_batch["x0"][0] 
+        x1_1s = main_batch["x1_1"][0] # training endpoint
+        x1_2s = main_batch["x1_2"][0] # unseen endpoint
+        #x1s = torch.cat([x1_1s, x1_2s], dim=0) # (M1+M2,G) or (B,G)
+        dataset_full = main_batch["dataset"][0] # (M,G)
+
+        device = x0s.device
+
+        #B, N, G = x0s.shape
+        N    = self.args.num_particles
+        T    = self.args.num_steps
+        G    = self.args.dim
+        gamma = float(self.args.friction)
+        kT    = float(getattr(self.args, "kT", 0.0))
+        ell   = float(getattr(self.args, "adj_length_scale", 1.0))
+        noise_scale = (0.0 if kT <= 0 else math.sqrt(2.0 * kT * self.dt / gamma))
+
+        # Ensure pools are (M,G)
+        if x1_1s.ndim == 3: x1_1s = x1_1s.reshape(-1, G)
+        if x1_2s.ndim == 3: x1_2s = x1_2s.reshape(-1, G)
+        
+        x0c_1, x1c_1, _ = make_aligned_clusters(self.ot_sampler, x0s, x1_1s, N, replace=True)   # to training endpoint
+        x0c_2, x1c_2, _ = make_aligned_clusters(self.ot_sampler, x0s, x1_2s, N, replace=True)   # to unseen endpoint
+
+        B = x0c_1.shape[0]
+
+        # rollout base-only dynamics (no bias)
+        def rollout_base(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+
+                # manifold/natural gradient towards target
+                F_nat, _ = natural_gradient_force(
+                    self.data_manifold_metric, pos, metric_samples=None, timestep=t
+                )                                             # (B,N,G)
+                base_force = F_nat
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * base_force + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+        # rollout bias-only
+        def rollout_bias_only(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+                if t == 0: 
+                    velocity = torch.zeros_like(pos)
+                else:
+                    velocity = (pos - traj[:, t-1]) / self.dt
+                
+                if self.vel_conditioned:
+                    # Use velocity direction (unit vector) instead of full velocity
+                    if self.dir_only:
+                        velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                        velocity_direction = velocity / (velocity_magnitude + 1e-8)
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity_direction.detach(), x1c.detach()
+                        ).detach()    
+                    else:
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity.detach(), x1c.detach()
+                        ).detach()
+                else:
+                    bias_force = self.bias_net(
+                        pos.detach(), x1c.detach()
+                    ).detach()   # (B,N,G)
+                    
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * (bias_force) + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+        # rollout bias+base (controlled dynamics)
+        def rollout_bias_plus_base(x0c, x1c):
+            pos  = x0c.clone()
+            traj = torch.empty((B, T+1, N, G), dtype=pos.dtype, device=pos.device)
+            traj[:, 0] = pos.clone()
+            for t in range(T):
+                if t == 0: 
+                    velocity = torch.zeros_like(pos)
+                else:
+                    velocity = (pos - traj[:, t-1]) / self.dt
+                    
+                F_nat, _ = natural_gradient_force(
+                    self.data_manifold_metric, pos, metric_samples=None, timestep=t
+                ) # (B,N,G)
+                base_force = F_nat
+                
+                if self.vel_conditioned:
+                    if self.dir_only:
+                        velocity_magnitude = torch.norm(velocity, dim=-1, keepdim=True)
+                        velocity_direction = velocity / (velocity_magnitude + 1e-8)
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity_direction.detach(), x1c.detach()
+                        ).detach()    
+                    else:
+                        bias_force = self.bias_net(
+                            pos.detach(), velocity.detach(), x1c.detach()
+                        ).detach()
+                else:
+                    bias_force = self.bias_net(
+                        pos.detach(), x1c.detach()
+                    ).detach()   # (B,N,G)
+                    
+                xi = torch.randn_like(pos) * noise_scale if noise_scale > 0 else 0.0
+                pos = pos + (self.dt / gamma) * (base_force + bias_force) + xi
+                traj[:, t+1] = pos.clone()
+            return traj  # (B,T+1,N,G)
+
+
+        traj_to_x1_1 = rollout_base(x0c_1, x1c_1)
+        traj_to_x1_2 = rollout_base(x0c_2, x1c_2)
+
+        # New:
+        traj_bias_only_x1_1 = rollout_bias_only(x0c_1, x1c_1)
+        traj_bias_plus_x1_1 = rollout_bias_plus_base(x0c_1, x1c_1)
+        traj_bias_only_x1_2 = rollout_bias_only(x0c_2, x1c_2)
+        traj_bias_plus_x1_2 = rollout_bias_plus_base(x0c_2, x1c_2)
+
+
+        # ---------- 4) Plot (first two dims) with targets as blue X ----------
+        save_dir = os.path.join(self.args.save_dir, "figures", self.args.data_name)
+        os.makedirs(save_dir, exist_ok=True)
+
+        ds2 = (dataset_full[:, :2].detach().cpu().numpy()
+               if isinstance(dataset_full, torch.Tensor) else dataset_full[:, :2])
+            
+        custom_colors_1 = ["#05009E", "#A19EFF", "#6B67EE"]
+        custom_colors_2 = ["#05009E", "#A19EFF", "#50B2D7"]
+        custom_cmap_1 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_1)
+        custom_cmap_2 = LinearSegmentedColormap.from_list("my_cmap", custom_colors_2)
+        
+        t0_data = self.timepoint_data["t0"]
+        t1_data = torch.cat([self.timepoint_data["t1_1"], self.timepoint_data["t1_2"]], 
+                            dim=0)
+        
+        # seen endpoint
+        self.plot_trajs(
+            traj_bias_only_x1_1,
+            "Bias-only → training endpoint (x1_1)",
+            f"{self.args.data_name}_bias_only_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_to_x1_1,
+            "Base-only trajectories → training endpoint (x1_1)",
+            f"{self.args.data_name}_base_only_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+        
+        self.plot_trajs(traj_bias_plus_x1_1,
+            "Bias + base trajectories → training endpoint (x1_1)",
+            f"{self.args.data_name}_bias_plus_base_to_x1_1.png",
+            x1c_1,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_1,
+            c_end='#6B67EE',
+            save_dir=save_dir
+        )
+
+        # unseen endpoint
+        self.plot_trajs(traj_to_x1_2,
+            "Base-only trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_base_only_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_only_x1_2,
+            "Bias-only trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_bias_only_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+        self.plot_trajs(traj_bias_plus_x1_2,
+            "Bias + base trajectories → unseen endpoint (x1_2)",
+            f"{self.args.data_name}_bias_plus_base_to_x1_2.png",
+            x1c_2,
+            timepoint_data={"t0": t0_data, "t1": t1_data},
+            cmap=custom_cmap_2,
+            c_end='#50B2D7',
+            save_dir=save_dir
+        )
+
+        def eval_cluster_set(traj_B_T1_N_G, targets_B_N_G, tag: str):
+            
+            finals = traj_B_T1_N_G[:, -1] # (B, N, G)
+            B = finals.shape[0]
+
+            # accumulate per-anchor metrics, then mean over B
+            per_b_vals = []
+            for b in range(B):
+                pred_b = finals[b].to(device) # (N, G)
+                true_b = targets_B_N_G[b].to(device)  # (N, G)
+                
+                names, vals = compute_distribution_distances(pred_b, true_b)
+                per_b_vals.append(vals)
+
+            per_b_vals = np.asarray(per_b_vals, dtype=float) # (B, num_metrics)
+            mean_vals   = per_b_vals.mean(axis=0)
+            std_vals    = per_b_vals.std(axis=0, ddof=1) if B > 1 else np.zeros_like(mean_vals)
+
+            # log (Lightning-friendly); also return a dict
+            out = {}
+            for n, m, s in zip(names, mean_vals, std_vals):
+                self.log(f"test/{tag}/{n}",  float(m), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                self.log(f"test/{tag}/{n}_std", float(s), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                out[f"{n}"] = float(m)
+                out[f"{n}_std"] = float(s)
+            return out
+
+
+        def eval_vs_full_distribution(traj_B_T1_N_G, full_target_distribution, tag: str):
+            
+            finals = traj_B_T1_N_G[:, -1] # (B, N, G)
+            
+            # Flatten all trajectory endpoints into single distribution
+            pred_all = finals.reshape(-1, G).to(device)  # (B*N, G)
+            true_all = full_target_distribution.to(device)  # (M, G)
+            
+            # Ensure both tensors are on the same device and have the right dtype
+            pred_all = pred_all.float()
+            true_all = true_all.float()
+            
+            # Resample to same size for MMD compatibility
+            names, vals = compute_wasserstein_distances(pred_all, true_all)
+            
+            # log results
+            out = {}
+            for n, v in zip(names, vals):
+                self.log(f"test/{tag}/{n}", float(v), on_step=False, on_epoch=True, prog_bar=False, logger=True)
+                out[f"{n}"] = float(v)
+            return out
+
+        # quantitative metrics over multiple independent simulations
+        num_sims = 5
+        base_seed = 12345
+
+        def run_one_sim(sim_idx: int):
+            # re-rollout all six variants with a distinct RNG state
+            devices = [device.index] if device.type == "cuda" and device.index is not None else None
+            with torch.random.fork_rng(devices=devices):
+                
+                torch.manual_seed(base_seed + sim_idx)
+
+                tr_base_11 = rollout_base(x0c_1, x1c_1)
+                tr_base_12 = rollout_base(x0c_2, x1c_2)
+
+                tr_bias_only_11 = rollout_bias_only(x0c_1, x1c_1)
+                tr_bias_plus_11 = rollout_bias_plus_base(x0c_1, x1c_1)
+
+                tr_bias_only_12 = rollout_bias_only(x0c_2, x1c_2)
+                tr_bias_plus_12 = rollout_bias_plus_base(x0c_2, x1c_2)
+
+            # evaluate per-cluster metrics (your helper returns a dict of means/std over B)
+            metrics = {}
+            metrics.update({f"base_x1_1/{k}": v for k, v in eval_cluster_set(tr_base_11,      x1c_1, "base/x1_1").items()})
+            metrics.update({f"base_x1_2/{k}": v for k, v in eval_cluster_set(tr_base_12,      x1c_2, "base/x1_2").items()})
+            metrics.update({f"bias_only_x1_1/{k}": v for k, v in eval_cluster_set(tr_bias_only_11, x1c_1, "bias_only/x1_1").items()})
+            metrics.update({f"bias_plus_x1_1/{k}": v for k, v in eval_cluster_set(tr_bias_plus_11, x1c_1, "bias_plus/x1_1").items()})
+            metrics.update({f"bias_only_x1_2/{k}": v for k, v in eval_cluster_set(tr_bias_only_12, x1c_2, "bias_only/x1_2").items()})
+            metrics.update({f"bias_plus_x1_2/{k}": v for k, v in eval_cluster_set(tr_bias_plus_12, x1c_2, "bias_plus/x1_2").items()})
+            
+            # evaluate vs full distributions
+            metrics.update({f"base_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_base_11, x1_1s, "base_vs_full/x1_1").items()})
+            metrics.update({f"base_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_base_12, x1_2s, "base_vs_full/x1_2").items()})
+            metrics.update({f"bias_only_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_bias_only_11, x1_1s, "bias_only_vs_full/x1_1").items()})
+            metrics.update({f"bias_plus_vs_full_x1_1/{k}": v for k, v in eval_vs_full_distribution(tr_bias_plus_11, x1_1s, "bias_plus_vs_full/x1_1").items()})
+            metrics.update({f"bias_only_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_bias_only_12, x1_2s, "bias_only_vs_full/x1_2").items()})
+            metrics.update({f"bias_plus_vs_full_x1_2/{k}": v for k, v in eval_vs_full_distribution(tr_bias_plus_12, x1_2s, "bias_plus_vs_full/x1_2").items()})
+            
+            return metrics
+
+        # run K sims and collect metrics per run
+        metrics_runs = [run_one_sim(k) for k in range(num_sims)]
+
+        agg = {}
+        all_keys = sorted(metrics_runs[0].keys())
+
+        for key in all_keys:
+            vals = torch.tensor([m[key] for m in metrics_runs], dtype=torch.float32)
+            agg[f"{key}_runs_mean"] = vals.mean().item()
+            agg[f"{key}_runs_std"]  = (vals.std(unbiased=True).item() if num_sims > 1 else 0.0)
+
+            # Log for Lightning
+            self.log(f"test/{key}_runs_mean", agg[f"{key}_runs_mean"], on_step=False, on_epoch=True, logger=True)
+            self.log(f"test/{key}_runs_std",  agg[f"{key}_runs_std"],  on_step=False, on_epoch=True, logger=True)
+
+        if getattr(self.trainer, "is_global_zero", True):
+            out_dir = os.path.join(self.args.save_dir, "metrics", self.args.data_name)
+            os.makedirs(out_dir, exist_ok=True)
+            stamp = time.strftime("%Y%m%d-%H%M%S")
+            with open(os.path.join(out_dir, f"test_metrics_aggregated_{num_sims}runs_{stamp}.json"), "w") as f:
+                json.dump(agg, f, indent=2)
+        
+        return {"num_traj": B}
+
+### REPLAY BUFFER ###     
+class ReplayBuffer:
+    def __init__(self, args):
+        BZ, T, N, G = args.buffer_size, args.num_steps, args.num_particles, args.dim
+        self.positions = torch.zeros((BZ, T+1, N, G), device=args.device)
+        self.target_positions = torch.zeros((BZ, N,   G), device=args.device)
+        self.forces = torch.zeros((BZ, T,   N, G), device=args.device)
+        self.log_tpm = torch.zeros((BZ,), device=args.device)
+        self.rewards = torch.zeros((BZ,), device=args.device)
+        self.batch_size, self.buffer_size, self.count = args.batch_size, args.buffer_size, 0
+
+    def add_ranked(self, data):
+        positions, target_positions, forces, log_tpm, rewards = data
+        # concat existing + new, keep top by reward
+        if self.count > 0:
+            pos = torch.cat([self.positions[:self.count], positions], dim=0)
+            tgt = torch.cat([self.target_positions[:self.count], target_positions], dim=0)
+            frc = torch.cat([self.forces[:self.count], forces], dim=0)
+            ltp = torch.cat([self.log_tpm[:self.count], log_tpm], dim=0)
+            rwd = torch.cat([self.rewards[:self.count], rewards], dim=0)
+        else:
+            pos, tgt, frc, ltp, rwd = positions, target_positions, forces, log_tpm, rewards
+        k = min(self.buffer_size, pos.size(0))
+        top_vals, top_idx = torch.topk(rwd, k=k, largest=True, sorted=False)
+        self.positions[:k] = pos.index_select(0, top_idx)
+        self.target_positions[:k] = tgt.index_select(0, top_idx)
+        self.forces[:k] = frc.index_select(0, top_idx)
+        self.log_tpm[:k] = ltp.index_select(0, top_idx)
+        self.rewards[:k] = top_vals
+        self.count = k
+
+    def sample(self):
+        assert self.count > 0, "buffer is empty"
+        idx = torch.randint(0, self.count, (self.batch_size,), device=self.positions.device)
+        return (
+            self.positions[idx], self.target_positions[idx],
+            self.forces[idx], self.log_tpm[idx], self.rewards[idx],
+        )
+
+### PATH OBJECTIVE ###
+class PathObjective:
+    def __init__(self, args):
+        self.dt = float(1.0 / args.num_steps)
+        self.gamma = args.friction
+        self.kT = getattr(args, "kT", 0.0)
+        self.sigma_v = math.sqrt(2.0 * self.kT / (self.gamma * self.dt))
+        self.log_prob = Normal(0.0, self.sigma_v).log_prob
+        self.sigma = args.sigma
+
+    def __call__(self, positions, target_positions, base_forces):
+        log_upm = self.unbiased_path_measure(positions, base_forces)
+        log_ri, final_idx = self.relaxed_indicator(positions, target_positions)
+        return log_upm + log_ri, final_idx, log_ri
+
+    def unbiased_path_measure(self, positions, base_forces):
+        v = (positions[:, 1:] - positions[:, :-1]) / self.dt # (B,T,N,G)
+        
+        means = base_forces / self.gamma # (B,T,N,G)
+        resid = v - means
+        return self.log_prob(resid).mean((1,2,3))
+
+    def relaxed_indicator(self, positions, target_positions):
+        # allow (B,N,G) or (B,T+1,N,G)
+        device = positions.device
+        if target_positions.ndim == 3:
+            target_positions = target_positions[:, None].expand_as(positions)
+            
+        target_positions = target_positions.to(device)
+        dist2  = (positions - target_positions).pow(2).mean((-2,-1)) # (B,T+1)
+        log_ri = -0.5 * dist2 / (self.sigma**2)
+        vals, idx = log_ri.max(dim=1)
+        return vals, idx

entangled-cell/environment.yml

@@ -0,0 +1,36 @@
+name: entangled-cell
+channels:
+  - conda-forge
+  - omnia
+  - defaults
+dependencies:
+  - python=3.10
+  - pytorch-cuda=12.4
+  - rdkit=2024.09.6
+  - seaborn
+  - torchmetrics
+  - numpy[version='>=1.26.0,<2.0.0']
+  - mctc-lib
+  - scikit-learn
+  - pyyaml
+  - jupyter
+  - ase
+  - python[version='>=3.10']
+  - tqdm
+  - dxtb
+  - openbabel=3.1.1
+  - pytorch-lightning>=2.0.0
+  - lightning>=2.0.0
+  - joblib
+  - pip
+  - pip:
+      - scipy==1.13.1
+      - wandb==0.22.1
+      - torchcfm==1.0.7
+      - pyemma==2.5.12
+      - torchdyn==1.0.6
+      - pot 
+
+  - jupyter
+  - ipykernel
+  - notebook

entangled-cell/eval.py

@@ -0,0 +1,276 @@
+
+# evaluation metrics
+import torch
+import math
+from functools import partial
+from typing import Optional
+
+import numpy as np
+import ot as pot
+import torch
+
+def wasserstein(
+    x0: torch.Tensor,
+    x1: torch.Tensor,
+    method: Optional[str] = None,
+    reg: float = 0.05,
+    power: int = 2,
+    **kwargs,
+) -> float:
+    assert power == 1 or power == 2
+    # ot_fn should take (a, b, M) as arguments where a, b are marginals and
+    # M is a cost matrix
+    if method == "exact" or method is None:
+        ot_fn = pot.emd2
+    elif method == "sinkhorn":
+        ot_fn = partial(pot.sinkhorn2, reg=reg)
+    else:
+        raise ValueError(f"Unknown method: {method}")
+
+    a, b = pot.unif(x0.shape[0]), pot.unif(x1.shape[0])
+    if x0.dim() > 2:
+        x0 = x0.reshape(x0.shape[0], -1)
+    if x1.dim() > 2:
+        x1 = x1.reshape(x1.shape[0], -1)
+    M = torch.cdist(x0, x1)
+    if power == 2:
+        M = M**2
+    ret = ot_fn(a, b, M.detach().cpu().numpy(), numItermax=1e7)
+    if power == 2:
+        ret = math.sqrt(ret)
+    return ret
+
+min_var_est = 1e-8
+
+
+# Consider linear time MMD with a linear kernel:
+# K(f(x), f(y)) = f(x)^Tf(y)
+# h(z_i, z_j) = k(x_i, x_j) + k(y_i, y_j) - k(x_i, y_j) - k(x_j, y_i)
+#             = [f(x_i) - f(y_i)]^T[f(x_j) - f(y_j)]
+#
+# f_of_X: batch_size * k
+# f_of_Y: batch_size * k
+def linear_mmd2(f_of_X, f_of_Y):
+    loss = 0.0
+    delta = f_of_X - f_of_Y
+    loss = torch.mean((delta[:-1] * delta[1:]).sum(1))
+    return loss
+
+
+# Consider linear time MMD with a polynomial kernel:
+# K(f(x), f(y)) = (alpha*f(x)^Tf(y) + c)^d
+# f_of_X: batch_size * k
+# f_of_Y: batch_size * k
+def poly_mmd2(f_of_X, f_of_Y, d=2, alpha=1.0, c=2.0):
+    K_XX = alpha * (f_of_X[:-1] * f_of_X[1:]).sum(1) + c
+    K_XX_mean = torch.mean(K_XX.pow(d))
+
+    K_YY = alpha * (f_of_Y[:-1] * f_of_Y[1:]).sum(1) + c
+    K_YY_mean = torch.mean(K_YY.pow(d))
+
+    K_XY = alpha * (f_of_X[:-1] * f_of_Y[1:]).sum(1) + c
+    K_XY_mean = torch.mean(K_XY.pow(d))
+
+    K_YX = alpha * (f_of_Y[:-1] * f_of_X[1:]).sum(1) + c
+    K_YX_mean = torch.mean(K_YX.pow(d))
+
+    return K_XX_mean + K_YY_mean - K_XY_mean - K_YX_mean
+
+
+def _mix_rbf_kernel(X, Y, sigma_list):
+    assert X.size(0) == Y.size(0)
+    m = X.size(0)
+
+    Z = torch.cat((X, Y), 0)
+    ZZT = torch.mm(Z, Z.t())
+    diag_ZZT = torch.diag(ZZT).unsqueeze(1)
+    Z_norm_sqr = diag_ZZT.expand_as(ZZT)
+    exponent = Z_norm_sqr - 2 * ZZT + Z_norm_sqr.t()
+
+    K = 0.0
+    for sigma in sigma_list:
+        gamma = 1.0 / (2 * sigma**2)
+        K += torch.exp(-gamma * exponent)
+
+    return K[:m, :m], K[:m, m:], K[m:, m:], len(sigma_list)
+
+
+def mix_rbf_mmd2(X, Y, sigma_list, biased=True):
+    K_XX, K_XY, K_YY, d = _mix_rbf_kernel(X, Y, sigma_list)
+    # return _mmd2(K_XX, K_XY, K_YY, const_diagonal=d, biased=biased)
+    return _mmd2(K_XX, K_XY, K_YY, const_diagonal=False, biased=biased)
+
+
+def mix_rbf_mmd2_and_ratio(X, Y, sigma_list, biased=True):
+    K_XX, K_XY, K_YY, d = _mix_rbf_kernel(X, Y, sigma_list)
+    # return _mmd2_and_ratio(K_XX, K_XY, K_YY, const_diagonal=d, biased=biased)
+    return _mmd2_and_ratio(K_XX, K_XY, K_YY, const_diagonal=False, biased=biased)
+
+
+################################################################################
+# Helper functions to compute variances based on kernel matrices
+################################################################################
+
+
+def _mmd2(K_XX, K_XY, K_YY, const_diagonal=False, biased=False):
+    m = K_XX.size(0)  # assume X, Y are same shape
+
+    # Get the various sums of kernels that we'll use
+    # Kts drop the diagonal, but we don't need to compute them explicitly
+    if const_diagonal is not False:
+        diag_X = diag_Y = const_diagonal
+        sum_diag_X = sum_diag_Y = m * const_diagonal
+    else:
+        diag_X = torch.diag(K_XX)  # (m,)
+        diag_Y = torch.diag(K_YY)  # (m,)
+        sum_diag_X = torch.sum(diag_X)
+        sum_diag_Y = torch.sum(diag_Y)
+
+    Kt_XX_sums = K_XX.sum(dim=1) - diag_X  # \tilde{K}_XX * e = K_XX * e - diag_X
+    Kt_YY_sums = K_YY.sum(dim=1) - diag_Y  # \tilde{K}_YY * e = K_YY * e - diag_Y
+    K_XY_sums_0 = K_XY.sum(dim=0)  # K_{XY}^T * e
+
+    Kt_XX_sum = Kt_XX_sums.sum()  # e^T * \tilde{K}_XX * e
+    Kt_YY_sum = Kt_YY_sums.sum()  # e^T * \tilde{K}_YY * e
+    K_XY_sum = K_XY_sums_0.sum()  # e^T * K_{XY} * e
+
+    if biased:
+        mmd2 = (
+            (Kt_XX_sum + sum_diag_X) / (m * m)
+            + (Kt_YY_sum + sum_diag_Y) / (m * m)
+            - 2.0 * K_XY_sum / (m * m)
+        )
+    else:
+        mmd2 = Kt_XX_sum / (m * (m - 1)) + Kt_YY_sum / (m * (m - 1)) - 2.0 * K_XY_sum / (m * m)
+
+    return mmd2
+
+
+def _mmd2_and_ratio(K_XX, K_XY, K_YY, const_diagonal=False, biased=False):
+    mmd2, var_est = _mmd2_and_variance(
+        K_XX, K_XY, K_YY, const_diagonal=const_diagonal, biased=biased
+    )
+    loss = mmd2 / torch.sqrt(torch.clamp(var_est, min=min_var_est))
+    return loss, mmd2, var_est
+
+
+def _mmd2_and_variance(K_XX, K_XY, K_YY, const_diagonal=False, biased=False):
+    m = K_XX.size(0)  # assume X, Y are same shape
+
+    # Get the various sums of kernels that we'll use
+    # Kts drop the diagonal, but we don't need to compute them explicitly
+    if const_diagonal is not False:
+        diag_X = diag_Y = const_diagonal
+        sum_diag_X = sum_diag_Y = m * const_diagonal
+        sum_diag2_X = sum_diag2_Y = m * const_diagonal**2
+    else:
+        diag_X = torch.diag(K_XX)  # (m,)
+        diag_Y = torch.diag(K_YY)  # (m,)
+        sum_diag_X = torch.sum(diag_X)
+        sum_diag_Y = torch.sum(diag_Y)
+        sum_diag2_X = diag_X.dot(diag_X)
+        sum_diag2_Y = diag_Y.dot(diag_Y)
+
+    Kt_XX_sums = K_XX.sum(dim=1) - diag_X  # \tilde{K}_XX * e = K_XX * e - diag_X
+    Kt_YY_sums = K_YY.sum(dim=1) - diag_Y  # \tilde{K}_YY * e = K_YY * e - diag_Y
+    K_XY_sums_0 = K_XY.sum(dim=0)  # K_{XY}^T * e
+    K_XY_sums_1 = K_XY.sum(dim=1)  # K_{XY} * e
+
+    Kt_XX_sum = Kt_XX_sums.sum()  # e^T * \tilde{K}_XX * e
+    Kt_YY_sum = Kt_YY_sums.sum()  # e^T * \tilde{K}_YY * e
+    K_XY_sum = K_XY_sums_0.sum()  # e^T * K_{XY} * e
+
+    Kt_XX_2_sum = (K_XX**2).sum() - sum_diag2_X  # \| \tilde{K}_XX \|_F^2
+    Kt_YY_2_sum = (K_YY**2).sum() - sum_diag2_Y  # \| \tilde{K}_YY \|_F^2
+    K_XY_2_sum = (K_XY**2).sum()  # \| K_{XY} \|_F^2
+
+    if biased:
+        mmd2 = (
+            (Kt_XX_sum + sum_diag_X) / (m * m)
+            + (Kt_YY_sum + sum_diag_Y) / (m * m)
+            - 2.0 * K_XY_sum / (m * m)
+        )
+    else:
+        mmd2 = Kt_XX_sum / (m * (m - 1)) + Kt_YY_sum / (m * (m - 1)) - 2.0 * K_XY_sum / (m * m)
+
+    var_est = (
+        2.0
+        / (m**2 * (m - 1.0) ** 2)
+        * (
+            2 * Kt_XX_sums.dot(Kt_XX_sums)
+            - Kt_XX_2_sum
+            + 2 * Kt_YY_sums.dot(Kt_YY_sums)
+            - Kt_YY_2_sum
+        )
+        - (4.0 * m - 6.0) / (m**3 * (m - 1.0) ** 3) * (Kt_XX_sum**2 + Kt_YY_sum**2)
+        + 4.0
+        * (m - 2.0)
+        / (m**3 * (m - 1.0) ** 2)
+        * (K_XY_sums_1.dot(K_XY_sums_1) + K_XY_sums_0.dot(K_XY_sums_0))
+        - 4.0 * (m - 3.0) / (m**3 * (m - 1.0) ** 2) * (K_XY_2_sum)
+        - (8 * m - 12) / (m**5 * (m - 1)) * K_XY_sum**2
+        + 8.0
+        / (m**3 * (m - 1.0))
+        * (
+            1.0 / m * (Kt_XX_sum + Kt_YY_sum) * K_XY_sum
+            - Kt_XX_sums.dot(K_XY_sums_1)
+            - Kt_YY_sums.dot(K_XY_sums_0)
+        )
+    )
+    return mmd2, var_est
+
+from typing import Union
+def compute_distances(pred, true):
+    """Computes distances between vectors."""
+    mse = torch.nn.functional.mse_loss(pred, true).item()
+    me = math.sqrt(mse)
+    mae = torch.mean(torch.abs(pred - true)).item()
+    return mse, me, mae
+
+def compute_distribution_distances(pred: torch.Tensor, true: Union[torch.Tensor, list]):
+    """computes distances between distributions.
+
+    This handles jagged times as a list of tensors.
+    """
+    NAMES = [
+        "1-Wasserstein",
+        "2-Wasserstein",
+        "RBF_MMD",
+        "Mean_MSE",
+        "Mean_L2",
+        "Mean_L1",
+        "Median_MSE",
+        "Median_L2",
+        "Median_L1",
+        "Eq-EMD2",
+    ]
+    a = pred
+    b = true
+    pred_2d = pred[:, :2]
+    true_2d = true[:, :2]
+    w1 = wasserstein(pred_2d, true_2d, power=1)
+    w2 = wasserstein(pred_2d, true_2d, power=2)
+
+    mmd_rbf = mix_rbf_mmd2(a, b, sigma_list=[0.01, 0.1, 1, 10, 100]).item()
+    mean_dists = compute_distances(torch.mean(a, dim=0), torch.mean(b, dim=0))
+    median_dists = compute_distances(torch.median(a, dim=0)[0], torch.median(b, dim=0)[0])
+    dists = [w1, w2, mmd_rbf, *mean_dists, *median_dists]
+    return NAMES, dists
+
+
+def compute_wasserstein_distances(pred: torch.Tensor, true: Union[torch.Tensor, list]):
+    """computes distances between distributions.
+
+    This handles jagged times as a list of tensors.
+    """
+    NAMES = [
+        "1-Wasserstein",
+        "2-Wasserstein",
+    ]
+    pred_2d = pred[:, :2]
+    true_2d = true[:, :2]
+    w1 = wasserstein(pred_2d, true_2d, power=1)
+    w2 = wasserstein(pred_2d, true_2d, power=2)
+    
+    dists = [w1, w2]
+    return NAMES, dists

entangled-cell/geo_metrics/land.py

@@ -0,0 +1,28 @@
+### Adapted from Metric Flow Matching (https://github.com/kkapusniak/metric-flow-matching)
+
+import torch
+
+
+def weighting_function(x, samples, gamma):
+    pairwise_sq_diff = (x[:, None, :] - samples[None, :, :]) ** 2
+    pairwise_sq_dist = pairwise_sq_diff.sum(-1)
+    weights = torch.exp(-pairwise_sq_dist / (2 * gamma**2))
+    return weights
+
+
+def land_metric_tensor(x, samples, gamma, rho):
+    weights = weighting_function(x, samples, gamma)  # Shape [B, N]
+    differences = samples[None, :, :] - x[:, None, :]  # Shape [B, N, D]
+    squared_differences = differences**2  # Shape [B, N, D]
+
+    # Compute the sum of weighted squared differences for each dimension
+    M_dd_diag = torch.einsum("bn,bnd->bd", weights, squared_differences) + rho
+
+    # Invert the metric tensor diagonal for each x_t
+    M_dd_inv_diag = 1.0 / M_dd_diag  # Shape [B, D] since it's diagonal
+    return M_dd_inv_diag
+
+
+def weighting_function_dt(x, dx_dt, samples, gamma, weights):
+    pairwise_sq_diff_dt = (x[:, None, :] - samples[None, :, :]) * dx_dt[:, None, :]
+    return -pairwise_sq_diff_dt.sum(-1) * weights / (gamma**2)

entangled-cell/geo_metrics/metric_factory.py

@@ -0,0 +1,162 @@
+### Adapted from Metric Flow Matching (https://github.com/kkapusniak/metric-flow-matching)
+
+import torch
+import pytorch_lightning as pl
+from pytorch_lightning.loggers import WandbLogger
+from torch.utils.data import Dataset, DataLoader
+
+
+from geo_metrics.land import land_metric_tensor
+from geo_metrics.rbf_unseen import RBFNetwork
+
+def unconditional_landscape_force(
+    data_manifold_metric, position, metric_samples, timestep=0, 
+    landscape_mode="metric_potential", eps=1e-6, unit_speed=False, target_speed=None
+):
+    # Call natural_gradient_force with dummy grad_phi
+    dummy_grad_phi = torch.zeros_like(position)
+    return natural_gradient_force(
+        data_manifold_metric, position, dummy_grad_phi, metric_samples, 
+        timestep=timestep, eps=eps, unit_speed=unit_speed, 
+        target_speed=target_speed, landscape_mode=landscape_mode
+    )
+
+def manifold_metric_diag(data_manifold_metric, position, metric_samples, timestep):
+    
+    B, N, G = position.shape
+    x_flat = position.reshape(B*N, G)  # (B*N, G)
+    M_flat = data_manifold_metric.calculate_metric(x_flat, metric_samples, timestep)  # (B*N, G)
+    return M_flat.view(B, N, -1)  # reshape back
+
+
+def natural_gradient_force(
+    data_manifold_metric, position, metric_samples, timestep=0,
+    eps=1e-6, unit_speed=False, target_speed=None
+):
+    B, N, G = position.shape
+    M_dd = manifold_metric_diag(data_manifold_metric, position, metric_samples, timestep=0)  # (B,N,G)
+    
+    position_grad = position.clone().requires_grad_(True)
+    M_dd_grad = manifold_metric_diag(data_manifold_metric, position_grad, metric_samples, timestep=0)
+    
+    # Create potential from metric: U = -sum(log(M_ii + eps))
+    potential = -(M_dd_grad + eps).log().sum()
+    
+    try:
+        grad_potential = torch.autograd.grad(
+            outputs=potential, 
+            inputs=position_grad, 
+            create_graph=False, 
+            retain_graph=False,
+            allow_unused=True
+        )[0]
+        
+        if grad_potential is not None:
+            u = -grad_potential / (M_dd.detach() + eps)
+        else:
+            u = torch.randn_like(position) / (M_dd + eps)
+    except:
+        u = torch.randn_like(position) / (M_dd + eps)
+
+    speed_M = torch.sqrt((u.pow(2) * M_dd.detach()).sum(dim=-1, keepdim=True).clamp_min(1e-24))  # (B,N,1)
+
+    if unit_speed:
+        if target_speed is None:
+            u = u / speed_M.clamp_min(1e-12)
+        else:
+            ts = (target_speed if torch.is_tensor(target_speed)
+                  else torch.tensor(target_speed, dtype=u.dtype, device=u.device))
+            u = u * (ts.view(1, 1, 1) / speed_M.clamp_min(1e-12))
+
+    return u, speed_M
+
+
+class DataManifoldMetric:
+    def __init__(
+        self,
+        args,
+        skipped_time_points=None,
+        datamodule=None,
+    ):
+        self.skipped_time_points = skipped_time_points
+        self.datamodule = datamodule
+
+        self.gamma = args.gamma
+        self.rho = args.rho
+        self.metric = args.velocity_metric
+        self.n_centers = args.n_centers
+        self.kappa = args.kappa
+        self.metric_epochs = args.metric_epochs
+        self.metric_patience = args.metric_patience
+        self.lr = args.metric_lr
+        self.alpha_metric = args.alpha_metric
+        self.image_data = args.data_type == "image"
+        self.accelerator = args.accelerator
+
+        self.called_first_time = True
+        self.args = args
+
+    def calculate_metric(self, x_t, samples, current_timestep):
+        if self.metric == "land":
+            M_dd_x_t = (
+                land_metric_tensor(x_t, samples, self.gamma, self.rho)
+                ** self.alpha_metric
+            )
+            
+        elif self.metric == "rbf":
+            if self.called_first_time:
+                self.rbf_networks = []
+                for timestep in range(self.datamodule.num_timesteps - 1):
+                    if timestep in self.skipped_time_points:
+                        continue
+                    print("Learning RBF networks, timestep: ", timestep)
+                    rbf_network = RBFNetwork(
+                        current_timestep=timestep,
+                        next_timestep=timestep
+                        + 1
+                        + (1 if timestep + 1 in self.skipped_time_points else 0),
+                        n_centers=self.n_centers,
+                        kappa=self.kappa,
+                        lr=self.lr,
+                        datamodule=self.datamodule,
+                        args=self.args
+                    )
+                    early_stop_callback = pl.callbacks.EarlyStopping(
+                        monitor="MetricModel/val_loss_learn_metric",
+                        patience=self.metric_patience,
+                        mode="min",
+                    )
+                    trainer = pl.Trainer(
+                        max_epochs=self.metric_epochs,
+                        accelerator=self.accelerator,
+                        logger=WandbLogger(),
+                        num_sanity_val_steps=0,
+                        callbacks=(
+                            [early_stop_callback] if not self.image_data else None
+                        ),
+                    )
+                    
+                    trainer.fit(rbf_network, self.datamodule)
+                    
+                    self.rbf_networks.append(rbf_network)
+                self.called_first_time = False
+                print("Learning RBF networksss... Done")
+            M_dd_x_t = self.rbf_networks[current_timestep].compute_metric(
+                x_t,
+                epsilon=self.rho,
+                alpha=self.alpha_metric,
+                image_hx=self.image_data,
+            )
+        return M_dd_x_t
+
+    def calculate_velocity(self, x_t, u_t, samples, timestep):
+
+        if len(u_t.shape) > 2:
+            u_t = u_t.reshape(u_t.shape[0], -1)
+            x_t = x_t.reshape(x_t.shape[0], -1)
+        M_dd_x_t = self.calculate_metric(x_t, samples, timestep).to(u_t.device)
+
+        velocity = torch.sqrt(((u_t**2) * M_dd_x_t).sum(dim=-1))
+        ut_sum = (u_t**2).sum(dim=-1)
+        metric_sum = M_dd_x_t.sum(dim=-1)
+        return velocity, ut_sum, metric_sum

entangled-cell/geo_metrics/rbf_unseen.py

@@ -0,0 +1,154 @@
+### Adapted from Metric Flow Matching (https://github.com/kkapusniak/metric-flow-matching)
+
+import pytorch_lightning as pl
+import torch
+from sklearn.cluster import KMeans
+import numpy as np
+
+
+class RBFNetwork(pl.LightningModule):
+    def __init__(
+        self,
+        current_timestep,
+        next_timestep,
+        n_centers: int = 100,
+        kappa: float = 1.0,
+        lr=1e-2,
+        datamodule=None,
+        image_data=False,
+        args=None
+    ):
+        super().__init__()
+        self.K = n_centers
+        self.current_timestep = current_timestep
+        self.next_timestep = next_timestep
+        self.clustering_model = KMeans(n_clusters=self.K)
+        self.kappa = kappa
+        self.last_val_loss = 1
+        self.lr = lr
+        self.W = torch.nn.Parameter(torch.rand(self.K, 1))
+        self.datamodule = datamodule
+        self.image_data = image_data
+        self.args = args
+
+    def on_before_zero_grad(self, *args, **kwargs):
+        self.W.data = torch.clamp(self.W.data, min=0.0001)
+
+    def on_train_start(self):
+        with torch.no_grad():
+            
+            batch = next(iter(self.trainer.datamodule.train_dataloader()))
+            """metric_samples_batch_filtered = [
+                x
+                for i, x in enumerate(batch[0]["metric_samples"][0])
+                if i in [self.current_timestep, self.next_timestep]
+            ]"""
+            metric_samples = batch[0]["metric_samples"][0]
+            all_data = torch.cat(metric_samples)
+            data_to_fit = all_data
+
+            print("Fitting Clustering model...")
+            self.clustering_model.fit(data_to_fit)
+
+            clusters = (
+                self.calculate_centroids(all_data, self.clustering_model.labels_)
+                if self.image_data
+                else self.clustering_model.cluster_centers_
+            )
+
+            self.C = torch.tensor(clusters, dtype=torch.float32).to(self.device)
+            labels = self.clustering_model.labels_
+            sigmas = np.zeros((self.K, 1))
+
+            for k in range(self.K):
+                points = all_data[labels == k, :]
+                variance = ((points - clusters[k]) ** 2).mean(axis=0)
+                sigmas[k, :] = np.sqrt(
+                    variance.sum() if self.image_data else variance.mean()
+                )
+
+            self.lamda = torch.tensor(
+                0.5 / (self.kappa * sigmas) ** 2, dtype=torch.float32
+            ).to(self.device)
+
+    def forward(self, x):
+        if len(x.shape) > 2:
+            x = x.reshape(x.shape[0], -1).to(self.C.device)
+        
+        x = x.to(self.C.device)
+        dist2 = torch.cdist(x, self.C) ** 2
+        self.phi_x = torch.exp(-0.5 * self.lamda[None, :, :] * dist2[:, :, None])
+        
+        h_x = (self.W.to(x.device) * self.phi_x).sum(dim=1)
+        return h_x
+
+    def training_step(self, batch, batch_idx):
+        main_batch = batch[0]["train_samples"][0]
+        
+        x0 = main_batch["x0"][0]
+        if not self.args.unseen:
+            x1 = main_batch["x1"][0]
+            inputs = torch.cat([x0, x1], dim=0).to(self.device)
+        else:
+            x1_1 = main_batch["x1_1"][0]
+            x1_2 = main_batch["x1_2"][0]
+            
+            inputs = torch.cat([x0, x1_1, x1_2], dim=0).to(self.device)
+        
+        loss = ((1 - self.forward(inputs)) ** 2).mean()
+        self.log(
+            "MetricModel/train_loss_learn_metric",
+            loss,
+            on_step=True,
+            on_epoch=True,
+            prog_bar=True,
+        )
+        return loss
+
+    def validation_step(self, batch, batch_idx):
+        main_batch = batch[0]["val_samples"][0]
+        
+        x0 = main_batch["x0"][0]
+        if not self.args.unseen:
+            x1 = main_batch["x1"][0]
+            inputs = torch.cat([x0, x1], dim=0).to(self.device)
+        else:
+            x1_1 = main_batch["x1_1"][0]
+            x1_2 = main_batch["x1_2"][0]
+            
+            inputs = torch.cat([x0, x1_1, x1_2], dim=0).to(self.device)
+
+        h = self.forward(inputs)
+        
+        loss = ((1 - h) ** 2).mean()
+        self.log(
+            "MetricModel/val_loss_learn_metric",
+            loss,
+            on_step=True,
+            on_epoch=True,
+            prog_bar=True,
+        )
+        self.last_val_loss = loss.detach()
+        return loss
+
+    def calculate_centroids(self, all_data, labels):
+        unique_labels = np.unique(labels)
+        centroids = np.zeros((len(unique_labels), all_data.shape[1]))
+        for i, label in enumerate(unique_labels):
+            centroids[i] = all_data[labels == label].mean(axis=0)
+        return centroids
+
+    def configure_optimizers(self):
+        optimizer = torch.optim.Adam(self.parameters(), lr=self.lr)
+        return optimizer
+
+    def compute_metric(self, x, alpha=1, epsilon=1e-2, image_hx=False):
+        if epsilon < 0:
+            epsilon = (1 - self.last_val_loss.item()) / abs(epsilon)
+        h_x = self.forward(x)
+        if image_hx:
+            h_x = 1 - torch.abs(1 - h_x)
+            M_x = 1 / (h_x**alpha + epsilon)
+        else:
+            M_x = 1 / (h_x + epsilon) ** alpha
+        return M_x

entangled-cell/parser.py

@@ -0,0 +1,156 @@
+import argparse
+
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--config_path", type=str, 
+        default='', 
+        help="Path to config file"
+    )
+    parser.add_argument(
+        "--optimal_transport_method",
+        type=str,
+        default="exact",
+        help="Use optimal transport in CFM training",
+    )
+    parser.add_argument(
+        "--split_ratios",
+        nargs=2,
+        type=float,
+        default=[0.9, 0.1],
+        help="Split ratios for training/validation data in CFM training",
+    )
+    parser.add_argument(
+        "--accelerator", type=str, default="cpu", help="Training accelerator"
+    )
+    parser.add_argument("--date", type=str)
+    parser.add_argument("--seed", default=2, type=int)
+    parser.add_argument("--device", default="cuda:1", type=str)
+    parser.add_argument("--molecule", default="aldp", type=str)
+    parser.add_argument('--wandb', action='store_true', default=False)
+    parser.add_argument('--unseen', action='store_true', default=False)
+    parser.add_argument('--run_name', default=None, type=str)
+    # Logger Config
+    parser.add_argument("--save_dir", default="", type=str)
+    parser.add_argument("--root_dir", default="", type=str)
+    # Policy Config
+    parser.add_argument("--bias", default="force", type=str)
+    # Sampling Config
+    parser.add_argument("--start_state", default="c5", type=str)
+    parser.add_argument("--end_state", default="c7ax", type=str)
+    parser.add_argument("--num_steps", default=100, type=int)
+    #parser.add_argument("--timestep", default=1, type=float)
+    parser.add_argument("--sigma", default=0.1, type=float)
+    parser.add_argument("--num_samples", default=16, type=int)
+    parser.add_argument("--temperature", default=300, type=float)
+    parser.add_argument("--friction", default=2.0, type=float)
+    parser.add_argument("--rbf", action='store_true', default=False)
+    parser.add_argument("--use_delta_to_target", action='store_true', default=False)
+    parser.add_argument("--use_gnn", action='store_true', default=False)
+    # Training Config
+    parser.add_argument("--start_temperature", default=600, type=float)
+    parser.add_argument("--end_temperature", default=300, type=float)
+    parser.add_argument("--num_rollouts", default=1000, type=int)
+    parser.add_argument("--trains_per_rollout", default=1000, type=int)
+    parser.add_argument("--log_z_lr", default=1e-3, type=float)
+    parser.add_argument("--policy_lr", default=1e-4, type=float)
+    parser.add_argument("--batch_size", default=64, type=int)
+    parser.add_argument("--buffer_size", default=1000, type=int)
+    parser.add_argument("--max_grad_norm", default=1, type=int)
+    parser.add_argument("--control_variate", default="global", type=str)
+    parser.add_argument("--self_normalize", action='store_true', default=False)
+    # path objective
+    parser.add_argument("--objective", default="ce", type=str)
+    parser.add_argument("--vel_conditioned", action='store_true', default=False)
+    parser.add_argument("--dir_only", action='store_true', default=False)
+    
+    # cell experiment
+    parser.add_argument("--num_particles", default=16, type=int)
+    #parser.add_argument("--gene_dim", default=50, type=int)
+    parser.add_argument("--kT", type=float, default=0.0)
+    ######### DATASETS #################
+    parser = datasets_parser(parser)
+
+    ######### METRICS ##################
+    parser = metric_parser(parser)
+
+    return parser.parse_args()
+
+
+def datasets_parser(parser):
+    parser.add_argument("--dim", type=int, default=50, help="Dimension of data")
+
+    parser.add_argument(
+        "--data_type",
+        type=str,
+        default="tahoe",
+        help="Type of data, now wither scrna or one of toys",
+    )
+    parser.add_argument(
+        "--data_name",
+        type=str,
+        default="tahoe",
+        help="Path to the dataset",
+    )
+    return parser
+
+
+def metric_parser(parser):
+    parser.add_argument(
+        "--n_centers",
+        type=int,
+        default=300,
+        help="Number of centers for RBF network",
+    )
+    parser.add_argument(
+        "--kappa",
+        type=float,
+        default=1.5,
+        help="Kappa parameter for RBF network",
+    )
+    parser.add_argument(
+        "--rho",
+        type=float,
+        default=-2.75,
+        help="Rho parameter in Riemanian Velocity Calculation",
+    )
+    parser.add_argument(
+        "--velocity_metric",
+        type=str,
+        default="rbf",
+        help="Metric for velocity calculation",
+    )
+    parser.add_argument(
+        "--gamma",
+        nargs="+",
+        type=float,
+        default=0.2,
+        help="Gamma parameter in Riemanian Velocity Calculation",
+    )
+    parser.add_argument(
+        "--metric_epochs",
+        type=int,
+        default=200,
+        help="Number of epochs for metric learning",
+    )
+    parser.add_argument(
+        "--metric_patience",
+        type=int,
+        default=25,
+        help="Patience for metric learning",
+    )
+    parser.add_argument(
+        "--metric_lr",
+        type=float,
+        default=1e-2,
+        help="Learning rate for metric learning",
+    )
+    parser.add_argument(
+        "--alpha_metric",
+        type=float,
+        default=1.0,
+        help="Alpha parameter for metric learning",
+    )
+    return parser
+

entangled-cell/scripts/clonidine100.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+HOME_LOC=/path/to/your/home/EntangledSBM
+ENV_LOC=/path/to/your/envs/entangled-cell
+SCRIPT_LOC=$HOME_LOC/entangled-cell
+LOG_LOC=$HOME_LOC/entangled-cell/logs
+DATE=$(date +%m_%d)
+SPECIAL_PREFIX='clonidine-ce-100D'
+PYTHON_EXECUTABLE=$ENV_LOC/bin/python
+
+# ===================================================================
+source "$(conda info --base)/etc/profile.d/conda.sh"
+conda activate $ENV_LOC
+
+$PYTHON_EXECUTABLE $SCRIPT_LOC/train_cell.py \
+    --config_path "$SCRIPT_LOC/configs/clonidine_100D.yaml" \
+    --save_dir "$SCRIPT_LOC/results/$DATE-clonidine-ce-100D" \
+    --root_dir "$SCRIPT_LOC" \
+    --wandb \
+    --device "cuda:0" \
+    --run_name "clonidine-ce-100D" \
+    --date "$DATE-clonidine-ce-100D" \
+    --num_rollouts 100 \
+    --num_steps 100 \
+    --use_delta_to_target \
+    --objective "ce" \
+    --sigma 0.1 \
+    --num_samples 64 \
+    --self_normalize \
+    --kT 0.05 \
+    --unseen \
+    --num_particles 16 \
+    --batch_size 64 \
+    --friction 2.0 \
+    --vel_conditioned >> ${LOG_LOC}/${DATE}_${SPECIAL_PREFIX}_train.log 2>&1
+
+conda deactivate

entangled-cell/scripts/clonidine150.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+HOME_LOC=/path/to/your/home/EntangledSBM
+ENV_LOC=/path/to/your/envs/entangled-cell
+SCRIPT_LOC=$HOME_LOC/entangled-cell
+LOG_LOC=$HOME_LOC/entangled-cell/logs
+DATE=$(date +%m_%d)
+SPECIAL_PREFIX='clonidine-ce-150D'
+PYTHON_EXECUTABLE=$ENV_LOC/bin/python
+
+# ===================================================================
+source "$(conda info --base)/etc/profile.d/conda.sh"
+conda activate $ENV_LOC
+
+$PYTHON_EXECUTABLE $SCRIPT_LOC/train_cell.py \
+    --config_path "$SCRIPT_LOC/configs/clonidine_150D.yaml" \
+    --save_dir "$SCRIPT_LOC/results/$DATE-clonidine-ce-150D" \
+    --root_dir "$SCRIPT_LOC" \
+    --wandb \
+    --device "cuda:0" \
+    --run_name "clonidine-ce-150D" \
+    --date "$DATE-clonidine-ce-150D" \
+    --num_rollouts 100 \
+    --num_steps 100 \
+    --use_delta_to_target \
+    --objective "ce" \
+    --sigma 0.1 \
+    --num_samples 64 \
+    --self_normalize \
+    --kT 0.1 \
+    --unseen \
+    --num_particles 16 \
+    --batch_size 64 \
+    --friction 2.0 \
+    --vel_conditioned >> ${LOG_LOC}/${DATE}_${SPECIAL_PREFIX}_train.log 2>&1
+
+conda deactivate

entangled-cell/scripts/clonidine50.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+HOME_LOC=/path/to/your/home/EntangledSBM
+ENV_LOC=/path/to/your/envs/entangled-cell
+SCRIPT_LOC=$HOME_LOC/entangled-cell
+LOG_LOC=$HOME_LOC/entangled-cell/logs
+DATE=$(date +%m_%d)
+SPECIAL_PREFIX='clonidine-ce-50D'
+PYTHON_EXECUTABLE=$ENV_LOC/bin/python
+
+# ===================================================================
+source "$(conda info --base)/etc/profile.d/conda.sh"
+conda activate $ENV_LOC
+
+$PYTHON_EXECUTABLE $SCRIPT_LOC/train_cell.py \
+    --config_path "$SCRIPT_LOC/configs/clonidine_50D.yaml" \
+    --save_dir "$SCRIPT_LOC/results/$DATE-clonidine-ce-50D" \
+    --root_dir "$SCRIPT_LOC" \
+    --wandb \
+    --device "cuda:0" \
+    --run_name "clonidine-ce-50D" \
+    --date "$DATE-clonidine-ce-50D" \
+    --num_rollouts 100 \
+    --num_steps 100 \
+    --use_delta_to_target \
+    --objective "ce" \
+    --sigma 0.1 \
+    --num_samples 64 \
+    --self_normalize \
+    --kT 0.1 \
+    --unseen \
+    --num_particles 16 \
+    --batch_size 64 \
+    --friction 2.0 \
+    --vel_conditioned >> ${LOG_LOC}/${DATE}_${SPECIAL_PREFIX}_train.log 2>&1
+
+conda deactivate

entangled-cell/scripts/trametinib.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+HOME_LOC=/path/to/your/home/EntangledSBM
+ENV_LOC=/path/to/your/envs/entangled-cell
+SCRIPT_LOC=$HOME_LOC/entangled-cell
+LOG_LOC=$HOME_LOC/entangled-cell/logs
+DATE=$(date +%m_%d)
+SPECIAL_PREFIX='trametinib-ce-50D'
+PYTHON_EXECUTABLE=$ENV_LOC/bin/python
+
+# ===================================================================
+source "$(conda info --base)/etc/profile.d/conda.sh"
+conda activate $ENV_LOC
+
+$PYTHON_EXECUTABLE $SCRIPT_LOC/train_cell.py \
+    --config_path "$SCRIPT_LOC/configs/trametinib_50D.yaml" \
+    --save_dir "$SCRIPT_LOC/results/$DATE-trametinib-ce-50D" \
+    --root_dir "$SCRIPT_LOC" \
+    --wandb \
+    --device "cuda:0" \
+    --run_name "trametinib-ce-50D" \
+    --date "$DATE-trametinib-ce-50D" \
+    --num_rollouts 100 \
+    --num_steps 100 \
+    --use_delta_to_target \
+    --objective "ce" \
+    --sigma 0.1 \
+    --num_samples 64 \
+    --self_normalize \
+    --kT 0.1 \
+    --unseen \
+    --num_particles 16 \
+    --batch_size 64 \
+    --friction 2.0 \
+    --vel_conditioned >> ${LOG_LOC}/${DATE}_${SPECIAL_PREFIX}_train.log 2>&1
+
+conda deactivate

entangled-cell/train_cell.py

@@ -0,0 +1,104 @@
+import os
+import sys
+os.environ["CUDA_VISIBLE_DEVICES"] = "6"
+
+import torch
+import wandb
+
+from entangledcell_module_unseen import EntangledNetTrainCellUnseen
+from entangledcell_module_three import EntangledNetTrainCellThree
+
+# cell
+from dataloaders.three_branch_data import ThreeBranchTahoeDataModule
+from dataloaders.clonidine_v2_data import ClonidineV2DataModule
+
+from geo_metrics.metric_factory import DataManifoldMetric
+from pytorch_lightning.loggers import WandbLogger
+from pytorch_lightning import Trainer
+
+from torchcfm.optimal_transport import OTPlanSampler
+from parser import parse_args
+from train_utils import load_config, merge_config
+from bias import BiasForceTransformer, BiasForceTransformerNoVel
+
+def main():
+    
+    args = parse_args()
+    if args.config_path:
+        config = load_config(args.config_path)
+        args = merge_config(args, config)
+    
+    args.training = True
+    args.save_dir = args.save_dir
+    
+    # Create positions directory for saving trajectory samples
+    positions_dir = f"{args.save_dir}/positions"
+    if not os.path.exists(positions_dir):
+        os.makedirs(positions_dir)
+            
+    wandb.init(project="entangled-cell", 
+                config=args, 
+                name=args.run_name)
+        
+    torch.manual_seed(args.seed)
+    
+    ot_sampler = (
+        OTPlanSampler(method=args.optimal_transport_method)
+        if args.optimal_transport_method != "None"
+        else None
+    )
+    
+    # get data
+    if args.data_name == "trametinib":
+        datamodule = ThreeBranchTahoeDataModule(args=args)
+    else:
+         datamodule = ClonidineV2DataModule(args=args)
+        
+    # data manifold metrics
+    data_manifold_metric = DataManifoldMetric(
+        args=args,
+        skipped_time_points=[],
+        datamodule=datamodule,
+    )
+    
+    if args.vel_conditioned:
+        bias_net = BiasForceTransformer(args)
+    else:
+        print("Using no velocity conditioned model")
+        bias_net = BiasForceTransformerNoVel(args)
+    
+    timepoint_data = datamodule.get_timepoint_data()
+    
+    if args.data_name == "trametinib":
+        entangled_train = EntangledNetTrainCellThree(args=args,
+                                            bias_net=bias_net,
+                                            data_manifold_metric=data_manifold_metric,
+                                            timepoint_data=timepoint_data,
+                                            ot_sampler=ot_sampler,
+                                            vel_conditioned=args.vel_conditioned)
+    else:
+        entangled_train = EntangledNetTrainCellUnseen(args=args,
+                                            bias_net=bias_net,
+                                            data_manifold_metric=data_manifold_metric,
+                                            timepoint_data=timepoint_data,
+                                            ot_sampler=ot_sampler,
+                                            vel_conditioned=args.vel_conditioned)
+    
+    wandb_logger = WandbLogger()
+    
+    trainer = Trainer(
+        max_epochs=args.num_rollouts,
+        logger=wandb_logger,
+        num_sanity_val_steps=0,
+        default_root_dir=args.root_dir,
+        gradient_clip_val=None,
+        devices=[0],
+    )
+    
+    trainer.fit(
+        entangled_train, datamodule=datamodule
+    )
+    trainer.test(entangled_train, datamodule=datamodule)
+
+if __name__ == "__main__":
+    main()

entangled-cell/train_utils.py

@@ -0,0 +1,115 @@
+import yaml
+import string
+import secrets
+import os
+
+import torch
+import wandb
+from pytorch_lightning.callbacks import Callback, EarlyStopping, ModelCheckpoint
+from torchdyn.core import NeuralODE
+
+import torch
+
+@torch.no_grad()
+def gather_local_starts(x0s, X0_pool, N, k=64):
+    # for each anchor b, take its k-NN from pool, then sample N distinct
+    B, G = x0s.shape
+    d2 = torch.cdist(x0s, X0_pool).pow(2)             # (B, M0)
+    knn_idx = d2.topk(k=min(k, X0_pool.size(0)), largest=False).indices  # (B,k)
+    x0_clusters = []
+    for b in range(B):
+        choices = knn_idx[b]
+        pick = choices[torch.randperm(choices.numel(), device=choices.device)[:N]]
+        x0_clusters.append(X0_pool[pick])             # (N,G)
+    return torch.stack(x0_clusters, dim=0)            # (B,N,G)
+
+@torch.no_grad()
+def make_aligned_clusters(ot_sampler, x0s, x1s, N, replace=True, k_local=128):
+    
+    device, dtype = x0s.device, x0s.dtype
+    
+    B, G = x0s.shape
+    M = x1s.shape[0]
+    # Use gather_local_starts to get N distinct cells for each source
+    x0_clusters = gather_local_starts(x0s, x0s, N, k=k_local).to(device=device, dtype=dtype)
+    x1_clusters = torch.empty((B, N, G), device=device, dtype=dtype)
+    idx1 = torch.empty((B, N), device=device, dtype=torch.long)
+
+    # Try to get a full coupling once (preferred: row-stochastic matrix P of shape (B, M))
+    P = None
+    if hasattr(ot_sampler, "coupling"):
+        P = ot_sampler.coupling(x0s, x1s)  # expected (B, M) torch tensor
+    elif hasattr(ot_sampler, "plan"):
+        P = ot_sampler.plan(x0s, x1s)      # same expectation
+    # If your ot_sampler only supports sampling, we’ll fall back row-by-row below.
+
+    for b in range(B):
+        x0_b = x0s[b:b+1]                  # (1, G)
+
+        if P is not None:
+            # --- Sample N targets from the row distribution P[b] ---
+            probs = P[b].clamp_min(0)
+            probs = probs / probs.sum().clamp_min(1e-12)
+            if replace:
+                j = torch.multinomial(probs, num_samples=N, replacement=True)   # (N,)
+            else:
+                k = min(N, (probs > 0).sum().item())
+                j = torch.multinomial(probs, num_samples=k, replacement=False)
+                if k < N:  # pad by repeating the last choice to keep shape
+                    j = torch.cat([j, j[-1:].expand(N-k)], dim=0)
+            x1_match = x1s[j]              # (N, G)
+        else:
+            # --- Row-wise fallback using sampler’s own sampling API ---
+            # Try to ask for N pairs at once
+            got = False
+            if hasattr(ot_sampler, "sample_plan"):
+                try:
+                    # many samplers support an argument like n_pairs / k / n
+                    x0_rep, x1_match = ot_sampler.sample_plan(
+                        x0_b, x1s, replace=replace, n_pairs=N
+                    )
+                    # x0_rep: (N, G) or (1, N, G) -> squeeze if needed
+                    x1_match = x1_match.view(N, G)
+                    got = True
+                except TypeError:
+                    pass
+            if not got:
+                # last resort: call sample_plan N times
+                xs, ys, js = [], [], []
+                for _ in range(N):
+                    x0_rep, x1_one = ot_sampler.sample_plan(x0_b, x1s, replace=replace)
+                    # infer index by nearest neighbor for bookkeeping (optional)
+                    j_hat = torch.cdist(x1_one.view(1, -1), x1s).argmin()
+                    xs.append(x0_rep.view(1, G))
+                    ys.append(x1_one.view(1, G))
+                    js.append(j_hat.view(1))
+                x1_match = torch.cat(ys, dim=0)
+                j = torch.cat(js, dim=0)
+
+        # Fill clusters (source row replicated N times)
+        #x0_clusters[b] = x0_b.expand(N, G)
+        x1_clusters[b] = x1_match
+        idx1[b] = j
+
+    return x0_clusters, x1_clusters, idx1
+
+
+def load_config(path):
+    with open(path, "r") as file:
+        config = yaml.safe_load(file)
+    return config
+
+
+def merge_config(args, config_updates):
+    for key, value in config_updates.items():
+        if not hasattr(args, key):
+            raise ValueError(
+                f"Unknown configuration parameter '{key}' found in the config file."
+            )
+        setattr(args, key, value)
+    return args
+
+
+def generate_group_string(length=16):
+    alphabet = string.ascii_letters + string.digits
+    return "".join(secrets.choice(alphabet) for _ in range(length))

entangled-tps/README.md

@@ -0,0 +1,69 @@
+# EntangledSBM for Transition Path Sampling ⚛️ 
+
+This part of the code is for running the transition path sampling (TPS) experiments. We demonstrate that EntanlgedSBM generates physically plausible transition paths for fast-folding proteins at an **all-atom resolution**. This codebase is partially built off of the [TPS-DPS repo](https://github.com/kiyoung98/tps-dps/tree/main).
+
+## Environment Installation
+```
+conda env create -f environment.yml
+
+conda activate entangled-tps
+```
+
+## Running Experiments
+
+All training scripts are located in `entangled-tps/scripts/`. Each script is pre-configured for a specific experiment.
+
+**Before running experiments:**
+
+1. Set `HOME_LOC` to the base path where EntangledSBM is located and `ENV_PATH` to the directory where your environment is downloaded in the `.bash` files in `scripts/`
+2. Replace `/path/to/your/home` to the base path where EntangledSBM is located in the `.slurm` files in `scripts/`
+3. Create a path `entangled-tps/results` where the simulated trajectory figures and metrics will be saved. Also, create `entangled-tps/logs` where the training logs will be saved.
+4. Activate the conda environment:
+```
+conda activate entangled-tps
+```
+5. Login to wandb using `wandb login`
+
+**Run experiment using `nohup` with the following commands:**
+
+```
+cd entangled-tps/scripts
+
+chmod aldp.sh
+
+nohup ./aldp.sh > aldp.log 2>&1 &
+```
+**Run experiment using `slurm` with the following commands:**
+```
+cd entangled-tps/scripts
+
+sbatch aldp.slurm
+```
+
+Evaluation will run automatically after each sampling step and logged with wandb.
+
+We report the following metrics in our paper:
+1. Root-Mean Squared Distance **(RMSD)** of the Kabsch-aligned coordinates averaged across 64 paths.
+2. Percentage of simulated trajectories that hit the target state **(THP)**
+3. Highest energy transition state along the biased trajectories averaged across the trajectories that hit the target **(ETS; kJ/mol)**
+
+## Overview of Outputs
+
+**Training outputs are saved to experiment-specific directories:**
+
+```
+entangled-tps/results/
+├── aldp_ce/
+│   └── positions/         # Generated trajectory
+│   └── paths.png          # Figure of simulated trajectories
+│   └── policy.pt          # Model checkpoint
+```
+
+**Training logs are saved in:**
+```
+entangled-tps/logs/
+├── <DATE>_entangled-aldp-ce.log
+├── <DATE>_entangled-chignolin-ce.log
+├── <DATE>_entangled-trpcage-ce.log
+└── <DATE>_entangled-bba-ce.log
+```

entangled-tps/data/aldp/c5.pdb

@@ -0,0 +1,41 @@
+REMARK   1 CREATED WITH OPENMM 7.1.1, 2017-09-12
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+HETATM   22  H3  NME A   3      18.270   9.740  19.934  1.00  0.00           H  
+TER      23      NME A   3
+
+CONECT    1    2
+CONECT    2    5    1    3    4
+CONECT    3    2
+CONECT    4    2
+CONECT    5    2    6    7
+CONECT    6    5
+CONECT    7    5
+CONECT   15   17
+CONECT   17   15   19   18
+CONECT   18   17
+CONECT   19   20   21   22   17
+CONECT   20   19
+CONECT   21   19
+CONECT   22   19
+END

entangled-tps/data/aldp/c7ax.pdb

@@ -0,0 +1,46 @@
+REMARK   1 CREATED WITH MDTraj 1.9.6, 2021-09-14
+CRYST1   20.233   20.233   20.233  90.00  90.00  90.00 P 1           1 
+MODEL        0
+ATOM      1  H1  ACE A   1      16.734  13.798  -5.063  1.00  0.00           H  
+ATOM      2  CH3 ACE A   1      16.819  14.884  -5.024  1.00  0.00           C  
+ATOM      3  H2  ACE A   1      16.937  15.273  -6.035  1.00  0.00           H  
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+ATOM     22  H3  NME A   3      12.874  13.900  -0.652  1.00  0.00           H  
+TER      23      NME A   3
+ENDMDL
+CONECT    1    2    2
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+CONECT   19   20   21   22
+CONECT   19   17   20   21   22
+CONECT   20   19   19
+CONECT   21   19   19
+CONECT   22   19   19
+END

entangled-tps/data/aldp/path.gro

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+oid sha256:1d4172aa7cba65dc8422ba41f104a25dcc7c44b903cfa64dc92e01c1dbf891f5
+size 573110

entangled-tps/data/bba/folded.pdb

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+TITLE     MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter
+CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1           1
+REMARK     285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET
+REMARK     285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION
+REMARK     285 WAS MISSING.
+REMARK     285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
+REMARK     285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON
+REMARK     285 THIS RECORD ARE MEANINGLESS.
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+ATOM      1  N   GLU A   1     -13.277  11.380  -1.109  1.00  0.00      A    N  
+ATOM      2  CA  GLU A   1     -13.673  10.089  -0.459  1.00  0.00      A    C  
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+ATOM      6  CG  GLU A   1     -15.087   7.999  -1.193  1.00  0.00      A    C  
+ATOM      7  CD  GLU A   1     -15.962   7.965   0.100  1.00  0.00      A    C  
+ATOM      8  OE1 GLU A   1     -15.508   8.544   1.143  1.00  0.00      A    O  
+ATOM      9  OE2 GLU A   1     -17.001   7.222   0.180  1.00  0.00      A    O  
+ATOM     10  H1  GLU A   1     -13.952  11.889  -1.662  1.00  0.00      A    H  
+ATOM     11  H2  GLU A   1     -12.498  11.203  -1.726  1.00  0.00      A    H  
+ATOM     12  H3  GLU A   1     -12.975  12.076  -0.443  1.00  0.00      A    H  
+ATOM     13  HA  GLU A   1     -14.346  10.228   0.387  1.00  0.00      A    H  
+ATOM     14  HB2 GLU A   1     -15.243  10.059  -1.848  1.00  0.00      A    H  
+ATOM     15  HB3 GLU A   1     -13.776   9.282  -2.430  1.00  0.00      A    H  
+ATOM     16  HG2 GLU A   1     -15.782   7.788  -2.006  1.00  0.00      A    H  
+ATOM     17  HG3 GLU A   1     -14.445   7.125  -1.088  1.00  0.00      A    H  
+ATOM     18  N   GLN A   2     -12.539   8.460   0.848  1.00  0.00      A    N  
+ATOM     19  CA  GLN A   2     -11.462   7.529   1.160  1.00  0.00      A    C  
+ATOM     20  C   GLN A   2     -11.681   6.117   0.379  1.00  0.00      A    C  
+ATOM     21  O   GLN A   2     -12.740   5.905  -0.186  1.00  0.00      A    O  
+ATOM     22  CB  GLN A   2     -11.340   7.287   2.608  1.00  0.00      A    C  
+ATOM     23  CG  GLN A   2     -10.881   8.536   3.381  1.00  0.00      A    C  
+ATOM     24  CD  GLN A   2     -10.778   8.409   4.966  1.00  0.00      A    C  
+ATOM     25  OE1 GLN A   2      -9.877   8.877   5.604  1.00  0.00      A    O  
+ATOM     26  NE2 GLN A   2     -11.661   7.721   5.593  1.00  0.00      A    N  
+ATOM     27  H   GLN A   2     -13.423   8.411   1.333  1.00  0.00      A    H  
+ATOM     28  HA  GLN A   2     -10.461   7.863   0.884  1.00  0.00      A    H  
+ATOM     29  HB2 GLN A   2     -12.336   6.958   2.904  1.00  0.00      A    H  
+ATOM     30  HB3 GLN A   2     -10.764   6.376   2.774  1.00  0.00      A    H  
+ATOM     31  HG2 GLN A   2      -9.865   8.759   3.057  1.00  0.00      A    H  
+ATOM     32  HG3 GLN A   2     -11.577   9.354   3.192  1.00  0.00      A    H  
+ATOM     33 HE21 GLN A   2     -12.262   7.143   5.025  1.00  0.00      A    H  
+ATOM     34 HE22 GLN A   2     -11.946   8.161   6.456  1.00  0.00      A    H  
+ATOM     35  N   TYR A   3     -10.671   5.132   0.478  1.00  0.00      A    N  
+ATOM     36  CA  TYR A   3     -10.647   3.992  -0.522  1.00  0.00      A    C  
+ATOM     37  C   TYR A   3     -10.323   2.663   0.071  1.00  0.00      A    C  
+ATOM     38  O   TYR A   3      -9.702   2.530   1.150  1.00  0.00      A    O  
+ATOM     39  CB  TYR A   3      -9.737   4.333  -1.691  1.00  0.00      A    C  
+ATOM     40  CG  TYR A   3      -8.334   4.976  -1.479  1.00  0.00      A    C  
+ATOM     41  CD1 TYR A   3      -7.522   4.494  -0.405  1.00  0.00      A    C  
+ATOM     42  CD2 TYR A   3      -7.947   6.112  -2.082  1.00  0.00      A    C  
+ATOM     43  CE1 TYR A   3      -6.407   5.224   0.000  1.00  0.00      A    C  
+ATOM     44  CE2 TYR A   3      -6.800   6.827  -1.778  1.00  0.00      A    C  
+ATOM     45  CZ  TYR A   3      -5.951   6.325  -0.743  1.00  0.00      A    C  
+ATOM     46  OH  TYR A   3      -4.797   7.008  -0.456  1.00  0.00      A    O  
+ATOM     47  H   TYR A   3      -9.812   5.408   0.930  1.00  0.00      A    H  
+ATOM     48  HA  TYR A   3     -11.621   3.943  -1.010  1.00  0.00      A    H  
+ATOM     49  HB2 TYR A   3      -9.632   3.481  -2.363  1.00  0.00      A    H  
+ATOM     50  HB3 TYR A   3     -10.347   5.039  -2.255  1.00  0.00      A    H  
+ATOM     51  HD1 TYR A   3      -7.872   3.651   0.170  1.00  0.00      A    H  
+ATOM     52  HD2 TYR A   3      -8.666   6.587  -2.732  1.00  0.00      A    H  
+ATOM     53  HE1 TYR A   3      -5.826   4.957   0.871  1.00  0.00      A    H  
+ATOM     54  HE2 TYR A   3      -6.580   7.815  -2.155  1.00  0.00      A    H  
+ATOM     55  HH  TYR A   3      -4.553   7.654  -1.123  1.00  0.00      A    H  
+ATOM     56  N   THR A   4     -10.666   1.616  -0.767  1.00  0.00      A    N  
+ATOM     57  CA  THR A   4     -10.382   0.214  -0.468  1.00  0.00      A    C  
+ATOM     58  C   THR A   4      -9.155  -0.295  -1.285  1.00  0.00      A    C  
+ATOM     59  O   THR A   4      -9.217  -1.388  -1.854  1.00  0.00      A    O  
+ATOM     60  CB  THR A   4     -11.648  -0.576  -0.740  1.00  0.00      A    C  
+ATOM     61  OG1 THR A   4     -11.955  -0.560  -2.119  1.00  0.00      A    O  
+ATOM     62  CG2 THR A   4     -12.888   0.019  -0.120  1.00  0.00      A    C  
+ATOM     63  H   THR A   4     -11.258   1.671  -1.583  1.00  0.00      A    H  
+ATOM     64  HA  THR A   4     -10.082   0.180   0.580  1.00  0.00      A    H  
+ATOM     65  HB  THR A   4     -11.676  -1.591  -0.343  1.00  0.00      A    H  
+ATOM     66  HG1 THR A   4     -11.191  -0.935  -2.562  1.00  0.00      A    H  
+ATOM     67 HG21 THR A   4     -12.695   0.293   0.918  1.00  0.00      A    H  
+ATOM     68 HG22 THR A   4     -13.646  -0.754   0.004  1.00  0.00      A    H  
+ATOM     69 HG23 THR A   4     -13.160   0.786  -0.845  1.00  0.00      A    H  
+ATOM     70  N   ALA A   5      -8.103   0.531  -1.348  1.00  0.00      A    N  
+ATOM     71  CA  ALA A   5      -6.841   0.236  -1.991  1.00  0.00      A    C  
+ATOM     72  C   ALA A   5      -6.291  -1.202  -1.731  1.00  0.00      A    C  
+ATOM     73  O   ALA A   5      -5.558  -1.413  -0.746  1.00  0.00      A    O  
+ATOM     74  CB  ALA A   5      -5.846   1.317  -1.458  1.00  0.00      A    C  
+ATOM     75  H   ALA A   5      -8.296   1.477  -1.050  1.00  0.00      A    H  
+ATOM     76  HA  ALA A   5      -6.980   0.529  -3.032  1.00  0.00      A    H  
+ATOM     77  HB1 ALA A   5      -6.405   2.214  -1.725  1.00  0.00      A    H  
+ATOM     78  HB2 ALA A   5      -4.933   1.269  -2.051  1.00  0.00      A    H  
+ATOM     79  HB3 ALA A   5      -5.717   1.260  -0.377  1.00  0.00      A    H  
+ATOM     80  N   LYS A   6      -6.602  -2.216  -2.595  1.00  0.00      A    N  
+ATOM     81  CA  LYS A   6      -6.165  -3.599  -2.409  1.00  0.00      A    C  
+ATOM     82  C   LYS A   6      -5.255  -4.211  -3.485  1.00  0.00      A    C  
+ATOM     83  O   LYS A   6      -5.318  -3.902  -4.664  1.00  0.00      A    O  
+ATOM     84  CB  LYS A   6      -7.414  -4.509  -2.311  1.00  0.00      A    C  
+ATOM     85  CG  LYS A   6      -8.462  -4.381  -3.436  1.00  0.00      A    C  
+ATOM     86  CD  LYS A   6      -9.654  -5.208  -3.189  1.00  0.00      A    C  
+ATOM     87  CE  LYS A   6     -10.882  -4.772  -3.998  1.00  0.00      A    C  
+ATOM     88  NZ  LYS A   6     -10.835  -5.035  -5.467  1.00  0.00      A    N  
+ATOM     89  H   LYS A   6      -7.221  -2.093  -3.384  1.00  0.00      A    H  
+ATOM     90  HA  LYS A   6      -5.588  -3.739  -1.495  1.00  0.00      A    H  
+ATOM     91  HB2 LYS A   6      -7.128  -5.560  -2.366  1.00  0.00      A    H  
+ATOM     92  HB3 LYS A   6      -7.884  -4.216  -1.372  1.00  0.00      A    H  
+ATOM     93  HG2 LYS A   6      -8.806  -3.354  -3.555  1.00  0.00      A    H  
+ATOM     94  HG3 LYS A   6      -8.043  -4.639  -4.408  1.00  0.00      A    H  
+ATOM     95  HD2 LYS A   6      -9.395  -6.255  -3.351  1.00  0.00      A    H  
+ATOM     96  HD3 LYS A   6      -9.957  -5.064  -2.152  1.00  0.00      A    H  
+ATOM     97  HE2 LYS A   6     -11.686  -5.378  -3.580  1.00  0.00      A    H  
+ATOM     98  HE3 LYS A   6     -11.077  -3.703  -3.922  1.00  0.00      A    H  
+ATOM     99  HZ1 LYS A   6     -10.564  -5.988  -5.663  1.00  0.00      A    H  
+ATOM    100  HZ2 LYS A   6     -10.147  -4.419  -5.877  1.00  0.00      A    H  
+ATOM    101  HZ3 LYS A   6     -11.729  -4.848  -5.899  1.00  0.00      A    H  
+ATOM    102  N   TYR A   7      -4.306  -5.072  -3.002  1.00  0.00      A    N  
+ATOM    103  CA  TYR A   7      -3.109  -5.382  -3.677  1.00  0.00      A    C  
+ATOM    104  C   TYR A   7      -2.660  -6.862  -3.301  1.00  0.00      A    C  
+ATOM    105  O   TYR A   7      -3.302  -7.611  -2.551  1.00  0.00      A    O  
+ATOM    106  CB  TYR A   7      -1.989  -4.512  -3.335  1.00  0.00      A    C  
+ATOM    107  CG  TYR A   7      -2.096  -3.076  -3.848  1.00  0.00      A    C  
+ATOM    108  CD1 TYR A   7      -2.737  -2.165  -2.998  1.00  0.00      A    C  
+ATOM    109  CD2 TYR A   7      -1.710  -2.735  -5.165  1.00  0.00      A    C  
+ATOM    110  CE1 TYR A   7      -2.924  -0.866  -3.472  1.00  0.00      A    C  
+ATOM    111  CE2 TYR A   7      -2.063  -1.424  -5.653  1.00  0.00      A    C  
+ATOM    112  CZ  TYR A   7      -2.617  -0.484  -4.786  1.00  0.00      A    C  
+ATOM    113  OH  TYR A   7      -2.967   0.733  -5.181  1.00  0.00      A    O  
+ATOM    114  H   TYR A   7      -4.343  -5.298  -2.018  1.00  0.00      A    H  
+ATOM    115  HA  TYR A   7      -3.259  -5.209  -4.742  1.00  0.00      A    H  
+ATOM    116  HB2 TYR A   7      -1.762  -4.620  -2.275  1.00  0.00      A    H  
+ATOM    117  HB3 TYR A   7      -1.125  -4.956  -3.829  1.00  0.00      A    H  
+ATOM    118  HD1 TYR A   7      -2.993  -2.379  -1.971  1.00  0.00      A    H  
+ATOM    119  HD2 TYR A   7      -1.251  -3.476  -5.803  1.00  0.00      A    H  
+ATOM    120  HE1 TYR A   7      -3.478  -0.243  -2.785  1.00  0.00      A    H  
+ATOM    121  HE2 TYR A   7      -2.021  -1.291  -6.724  1.00  0.00      A    H  
+ATOM    122  HH  TYR A   7      -2.782   1.432  -4.549  1.00  0.00      A    H  
+ATOM    123  N   LYS A   8      -1.529  -7.469  -3.831  1.00  0.00      A    N  
+ATOM    124  CA  LYS A   8      -0.846  -8.822  -3.561  1.00  0.00      A    C  
+ATOM    125  C   LYS A   8      -0.628  -9.270  -2.083  1.00  0.00      A    C  
+ATOM    126  O   LYS A   8       0.441  -9.097  -1.543  1.00  0.00      A    O  
+ATOM    127  CB  LYS A   8       0.452  -9.065  -4.389  1.00  0.00      A    C  
+ATOM    128  CG  LYS A   8       0.247  -8.653  -5.895  1.00  0.00      A    C  
+ATOM    129  CD  LYS A   8      -0.878  -9.429  -6.507  1.00  0.00      A    C  
+ATOM    130  CE  LYS A   8      -0.360 -10.870  -6.624  1.00  0.00      A    C  
+ATOM    131  NZ  LYS A   8      -0.859 -11.596  -7.842  1.00  0.00      A    N  
+ATOM    132  H   LYS A   8      -0.997  -6.881  -4.456  1.00  0.00      A    H  
+ATOM    133  HA  LYS A   8      -1.485  -9.636  -3.903  1.00  0.00      A    H  
+ATOM    134  HB2 LYS A   8       1.244  -8.375  -4.098  1.00  0.00      A    H  
+ATOM    135  HB3 LYS A   8       0.780 -10.099  -4.282  1.00  0.00      A    H  
+ATOM    136  HG2 LYS A   8       0.009  -7.592  -5.818  1.00  0.00      A    H  
+ATOM    137  HG3 LYS A   8       1.129  -8.879  -6.493  1.00  0.00      A    H  
+ATOM    138  HD2 LYS A   8      -1.790  -9.524  -5.918  1.00  0.00      A    H  
+ATOM    139  HD3 LYS A   8      -1.230  -8.961  -7.427  1.00  0.00      A    H  
+ATOM    140  HE2 LYS A   8       0.717 -10.955  -6.766  1.00  0.00      A    H  
+ATOM    141  HE3 LYS A   8      -0.558 -11.306  -5.645  1.00  0.00      A    H  
+ATOM    142  HZ1 LYS A   8      -1.787 -11.989  -7.774  1.00  0.00      A    H  
+ATOM    143  HZ2 LYS A   8      -0.251 -12.398  -7.914  1.00  0.00      A    H  
+ATOM    144  HZ3 LYS A   8      -0.781 -11.178  -8.758  1.00  0.00      A    H  
+ATOM    145  N   GLY A   9      -1.729  -9.823  -1.564  1.00  0.00      A    N  
+ATOM    146  CA  GLY A   9      -1.879 -10.239  -0.128  1.00  0.00      A    C  
+ATOM    147  C   GLY A   9      -2.642  -9.065   0.667  1.00  0.00      A    C  
+ATOM    148  O   GLY A   9      -3.771  -9.220   1.186  1.00  0.00      A    O  
+ATOM    149  H   GLY A   9      -2.560  -9.671  -2.118  1.00  0.00      A    H  
+ATOM    150  HA2 GLY A   9      -2.410 -11.189  -0.192  1.00  0.00      A    H  
+ATOM    151  HA3 GLY A   9      -0.864 -10.376   0.244  1.00  0.00      A    H  
+ATOM    152  N   ARG A  10      -1.969  -7.942   0.825  1.00  0.00      A    N  
+ATOM    153  CA  ARG A  10      -2.255  -6.824   1.680  1.00  0.00      A    C  
+ATOM    154  C   ARG A  10      -3.417  -5.930   1.177  1.00  0.00      A    C  
+ATOM    155  O   ARG A  10      -3.814  -6.103   0.033  1.00  0.00      A    O  
+ATOM    156  CB  ARG A  10      -1.001  -6.087   1.945  1.00  0.00      A    C  
+ATOM    157  CG  ARG A  10       0.133  -6.942   2.378  1.00  0.00      A    C  
+ATOM    158  CD  ARG A  10       1.471  -6.179   2.704  1.00  0.00      A    C  
+ATOM    159  NE  ARG A  10       2.580  -7.172   2.862  1.00  0.00      A    N  
+ATOM    160  CZ  ARG A  10       3.448  -7.127   3.869  1.00  0.00      A    C  
+ATOM    161  NH1 ARG A  10       3.418  -6.106   4.692  1.00  0.00      A    N  
+ATOM    162  NH2 ARG A  10       4.282  -8.045   3.991  1.00  0.00      A    N  
+ATOM    163  H   ARG A  10      -1.272  -7.764   0.117  1.00  0.00      A    H  
+ATOM    164  HA  ARG A  10      -2.529  -7.169   2.677  1.00  0.00      A    H  
+ATOM    165  HB2 ARG A  10      -0.725  -5.653   0.985  1.00  0.00      A    H  
+ATOM    166  HB3 ARG A  10      -1.127  -5.280   2.667  1.00  0.00      A    H  
+ATOM    167  HG2 ARG A  10      -0.140  -7.723   3.087  1.00  0.00      A    H  
+ATOM    168  HG3 ARG A  10       0.361  -7.641   1.573  1.00  0.00      A    H  
+ATOM    169  HD2 ARG A  10       1.952  -5.548   1.957  1.00  0.00      A    H  
+ATOM    170  HD3 ARG A  10       1.410  -5.594   3.622  1.00  0.00      A    H  
+ATOM    171  HE  ARG A  10       2.555  -8.054   2.370  1.00  0.00      A    H  
+ATOM    172 HH11 ARG A  10       2.625  -5.489   4.584  1.00  0.00      A    H  
+ATOM    173 HH12 ARG A  10       4.077  -6.065   5.456  1.00  0.00      A    H  
+ATOM    174 HH21 ARG A  10       4.416  -8.618   3.170  1.00  0.00      A    H  
+ATOM    175 HH22 ARG A  10       4.872  -8.176   4.800  1.00  0.00      A    H  
+ATOM    176  N   THR A  11      -4.061  -5.162   2.093  1.00  0.00      A    N  
+ATOM    177  CA  THR A  11      -4.972  -4.020   1.735  1.00  0.00      A    C  
+ATOM    178  C   THR A  11      -4.988  -2.916   2.847  1.00  0.00      A    C  
+ATOM    179  O   THR A  11      -4.888  -3.198   4.082  1.00  0.00      A    O  
+ATOM    180  CB  THR A  11      -6.352  -4.591   1.726  1.00  0.00      A    C  
+ATOM    181  OG1 THR A  11      -6.465  -5.376   0.508  1.00  0.00      A    O  
+ATOM    182  CG2 THR A  11      -7.476  -3.619   1.977  1.00  0.00      A    C  
+ATOM    183  H   THR A  11      -3.714  -5.218   3.040  1.00  0.00      A    H  
+ATOM    184  HA  THR A  11      -4.687  -3.569   0.785  1.00  0.00      A    H  
+ATOM    185  HB  THR A  11      -6.443  -5.302   2.547  1.00  0.00      A    H  
+ATOM    186  HG1 THR A  11      -5.585  -5.753   0.435  1.00  0.00      A    H  
+ATOM    187 HG21 THR A  11      -8.413  -4.144   1.790  1.00  0.00      A    H  
+ATOM    188 HG22 THR A  11      -7.400  -2.691   1.410  1.00  0.00      A    H  
+ATOM    189 HG23 THR A  11      -7.412  -3.364   3.035  1.00  0.00      A    H  
+ATOM    190  N   PHE A  12      -5.027  -1.600   2.437  1.00  0.00      A    N  
+ATOM    191  CA  PHE A  12      -4.892  -0.415   3.254  1.00  0.00      A    C  
+ATOM    192  C   PHE A  12      -6.045   0.590   3.075  1.00  0.00      A    C  
+ATOM    193  O   PHE A  12      -6.753   0.641   2.115  1.00  0.00      A    O  
+ATOM    194  CB  PHE A  12      -3.431   0.158   3.027  1.00  0.00      A    C  
+ATOM    195  CG  PHE A  12      -2.214  -0.818   2.850  1.00  0.00      A    C  
+ATOM    196  CD1 PHE A  12      -1.951  -1.340   1.571  1.00  0.00      A    C  
+ATOM    197  CD2 PHE A  12      -1.356  -1.041   3.929  1.00  0.00      A    C  
+ATOM    198  CE1 PHE A  12      -0.857  -2.170   1.323  1.00  0.00      A    C  
+ATOM    199  CE2 PHE A  12      -0.173  -1.863   3.660  1.00  0.00      A    C  
+ATOM    200  CZ  PHE A  12      -0.049  -2.472   2.427  1.00  0.00      A    C  
+ATOM    201  H   PHE A  12      -5.281  -1.474   1.468  1.00  0.00      A    H  
+ATOM    202  HA  PHE A  12      -4.977  -0.656   4.314  1.00  0.00      A    H  
+ATOM    203  HB2 PHE A  12      -3.385   0.990   2.325  1.00  0.00      A    H  
+ATOM    204  HB3 PHE A  12      -3.141   0.780   3.874  1.00  0.00      A    H  
+ATOM    205  HD1 PHE A  12      -2.522  -0.909   0.762  1.00  0.00      A    H  
+ATOM    206  HD2 PHE A  12      -1.505  -0.520   4.864  1.00  0.00      A    H  
+ATOM    207  HE1 PHE A  12      -0.661  -2.581   0.344  1.00  0.00      A    H  
+ATOM    208  HE2 PHE A  12       0.672  -2.034   4.309  1.00  0.00      A    H  
+ATOM    209  HZ  PHE A  12       0.740  -3.158   2.155  1.00  0.00      A    H  
+ATOM    210  N   ARG A  13      -6.038   1.514   4.058  1.00  0.00      A    N  
+ATOM    211  CA  ARG A  13      -6.966   2.662   4.237  1.00  0.00      A    C  
+ATOM    212  C   ARG A  13      -6.317   3.950   4.285  1.00  0.00      A    C  
+ATOM    213  O   ARG A  13      -7.052   4.927   4.192  1.00  0.00      A    O  
+ATOM    214  CB  ARG A  13      -7.760   2.513   5.582  1.00  0.00      A    C  
+ATOM    215  CG  ARG A  13      -9.220   3.071   5.592  1.00  0.00      A    C  
+ATOM    216  CD  ARG A  13     -10.103   2.143   4.841  1.00  0.00      A    C  
+ATOM    217  NE  ARG A  13     -10.379   0.944   5.729  1.00  0.00      A    N  
+ATOM    218  CZ  ARG A  13     -10.998  -0.109   5.259  1.00  0.00      A    C  
+ATOM    219  NH1 ARG A  13     -11.660  -0.132   4.126  1.00  0.00      A    N  
+ATOM    220  NH2 ARG A  13     -11.077  -1.200   5.906  1.00  0.00      A    N  
+ATOM    221  H   ARG A  13      -5.361   1.572   4.805  1.00  0.00      A    H  
+ATOM    222  HA  ARG A  13      -7.811   2.604   3.550  1.00  0.00      A    H  
+ATOM    223  HB2 ARG A  13      -7.846   1.470   5.888  1.00  0.00      A    H  
+ATOM    224  HB3 ARG A  13      -7.158   3.017   6.338  1.00  0.00      A    H  
+ATOM    225  HG2 ARG A  13      -9.535   3.211   6.626  1.00  0.00      A    H  
+ATOM    226  HG3 ARG A  13      -9.287   3.989   5.008  1.00  0.00      A    H  
+ATOM    227  HD2 ARG A  13     -11.018   2.728   4.749  1.00  0.00      A    H  
+ATOM    228  HD3 ARG A  13      -9.753   1.905   3.836  1.00  0.00      A    H  
+ATOM    229  HE  ARG A  13      -9.946   0.961   6.642  1.00  0.00      A    H  
+ATOM    230 HH11 ARG A  13     -11.829   0.655   3.515  1.00  0.00      A    H  
+ATOM    231 HH12 ARG A  13     -12.165  -0.985   3.932  1.00  0.00      A    H  
+ATOM    232 HH21 ARG A  13     -10.467  -1.359   6.695  1.00  0.00      A    H  
+ATOM    233 HH22 ARG A  13     -11.366  -2.012   5.380  1.00  0.00      A    H  
+ATOM    234  N   ASN A  14      -4.976   4.098   4.434  1.00  0.00      A    N  
+ATOM    235  CA  ASN A  14      -4.309   5.374   4.614  1.00  0.00      A    C  
+ATOM    236  C   ASN A  14      -2.956   5.321   3.757  1.00  0.00      A    C  
+ATOM    237  O   ASN A  14      -2.253   4.292   3.720  1.00  0.00      A    O  
+ATOM    238  CB  ASN A  14      -3.986   5.642   6.094  1.00  0.00      A    C  
+ATOM    239  CG  ASN A  14      -3.338   6.979   6.461  1.00  0.00      A    C  
+ATOM    240  OD1 ASN A  14      -2.128   7.111   6.351  1.00  0.00      A    O  
+ATOM    241  ND2 ASN A  14      -4.028   7.955   6.940  1.00  0.00      A    N  
+ATOM    242  H   ASN A  14      -4.355   3.330   4.642  1.00  0.00      A    H  
+ATOM    243  HA  ASN A  14      -4.862   6.228   4.225  1.00  0.00      A    H  
+ATOM    244  HB2 ASN A  14      -4.704   5.360   6.864  1.00  0.00      A    H  
+ATOM    245  HB3 ASN A  14      -3.257   4.894   6.406  1.00  0.00      A    H  
+ATOM    246 HD21 ASN A  14      -5.025   7.843   7.060  1.00  0.00      A    H  
+ATOM    247 HD22 ASN A  14      -3.495   8.812   6.984  1.00  0.00      A    H  
+ATOM    248  N   GLU A  15      -2.519   6.472   3.309  1.00  0.00      A    N  
+ATOM    249  CA  GLU A  15      -1.451   6.632   2.287  1.00  0.00      A    C  
+ATOM    250  C   GLU A  15      -0.002   6.459   2.806  1.00  0.00      A    C  
+ATOM    251  O   GLU A  15       0.855   5.881   2.167  1.00  0.00      A    O  
+ATOM    252  CB  GLU A  15      -1.695   7.981   1.560  1.00  0.00      A    C  
+ATOM    253  CG  GLU A  15      -0.589   8.540   0.736  1.00  0.00      A    C  
+ATOM    254  CD  GLU A  15      -0.651  10.113   0.740  1.00  0.00      A    C  
+ATOM    255  OE1 GLU A  15      -0.726  10.778   1.773  1.00  0.00      A    O  
+ATOM    256  OE2 GLU A  15      -0.654  10.650  -0.391  1.00  0.00      A    O  
+ATOM    257  H   GLU A  15      -3.045   7.254   3.671  1.00  0.00      A    H  
+ATOM    258  HA  GLU A  15      -1.511   5.834   1.546  1.00  0.00      A    H  
+ATOM    259  HB2 GLU A  15      -2.569   7.983   0.908  1.00  0.00      A    H  
+ATOM    260  HB3 GLU A  15      -1.814   8.684   2.385  1.00  0.00      A    H  
+ATOM    261  HG2 GLU A  15       0.352   8.368   1.258  1.00  0.00      A    H  
+ATOM    262  HG3 GLU A  15      -0.525   8.034  -0.228  1.00  0.00      A    H  
+ATOM    263  N   LYS A  16       0.179   6.747   4.098  1.00  0.00      A    N  
+ATOM    264  CA  LYS A  16       1.405   6.596   4.795  1.00  0.00      A    C  
+ATOM    265  C   LYS A  16       1.901   5.120   4.894  1.00  0.00      A    C  
+ATOM    266  O   LYS A  16       3.106   4.892   4.880  1.00  0.00      A    O  
+ATOM    267  CB  LYS A  16       1.233   7.275   6.136  1.00  0.00      A    C  
+ATOM    268  CG  LYS A  16       2.466   7.264   7.077  1.00  0.00      A    C  
+ATOM    269  CD  LYS A  16       2.087   6.289   8.313  1.00  0.00      A    C  
+ATOM    270  CE  LYS A  16       3.208   6.205   9.312  1.00  0.00      A    C  
+ATOM    271  NZ  LYS A  16       2.861   5.364  10.508  1.00  0.00      A    N  
+ATOM    272  H   LYS A  16      -0.582   7.171   4.608  1.00  0.00      A    H  
+ATOM    273  HA  LYS A  16       2.180   7.178   4.295  1.00  0.00      A    H  
+ATOM    274  HB2 LYS A  16       1.025   8.317   5.888  1.00  0.00      A    H  
+ATOM    275  HB3 LYS A  16       0.449   6.644   6.555  1.00  0.00      A    H  
+ATOM    276  HG2 LYS A  16       3.393   6.969   6.584  1.00  0.00      A    H  
+ATOM    277  HG3 LYS A  16       2.586   8.260   7.505  1.00  0.00      A    H  
+ATOM    278  HD2 LYS A  16       1.163   6.646   8.767  1.00  0.00      A    H  
+ATOM    279  HD3 LYS A  16       1.892   5.279   7.953  1.00  0.00      A    H  
+ATOM    280  HE2 LYS A  16       4.103   5.811   8.830  1.00  0.00      A    H  
+ATOM    281  HE3 LYS A  16       3.352   7.241   9.620  1.00  0.00      A    H  
+ATOM    282  HZ1 LYS A  16       2.783   4.366  10.377  1.00  0.00      A    H  
+ATOM    283  HZ2 LYS A  16       1.948   5.555  10.894  1.00  0.00      A    H  
+ATOM    284  HZ3 LYS A  16       3.593   5.482  11.194  1.00  0.00      A    H  
+ATOM    285  N   GLU A  17       0.960   4.171   5.196  1.00  0.00      A    N  
+ATOM    286  CA  GLU A  17       1.180   2.758   5.448  1.00  0.00      A    C  
+ATOM    287  C   GLU A  17       1.167   1.884   4.153  1.00  0.00      A    C  
+ATOM    288  O   GLU A  17       1.802   0.818   4.089  1.00  0.00      A    O  
+ATOM    289  CB  GLU A  17       0.065   2.126   6.253  1.00  0.00      A    C  
+ATOM    290  CG  GLU A  17      -0.043   2.543   7.799  1.00  0.00      A    C  
+ATOM    291  CD  GLU A  17       1.247   2.449   8.535  1.00  0.00      A    C  
+ATOM    292  OE1 GLU A  17       1.991   1.473   8.392  1.00  0.00      A    O  
+ATOM    293  OE2 GLU A  17       1.494   3.216   9.486  1.00  0.00      A    O  
+ATOM    294  H   GLU A  17       0.066   4.610   5.029  1.00  0.00      A    H  
+ATOM    295  HA  GLU A  17       2.117   2.794   6.003  1.00  0.00      A    H  
+ATOM    296  HB2 GLU A  17      -0.889   2.473   5.854  1.00  0.00      A    H  
+ATOM    297  HB3 GLU A  17       0.150   1.039   6.266  1.00  0.00      A    H  
+ATOM    298  HG2 GLU A  17      -0.367   3.582   7.861  1.00  0.00      A    H  
+ATOM    299  HG3 GLU A  17      -0.820   2.002   8.339  1.00  0.00      A    H  
+ATOM    300  N   LEU A  18       0.488   2.533   3.180  1.00  0.00      A    N  
+ATOM    301  CA  LEU A  18       0.421   2.015   1.815  1.00  0.00      A    C  
+ATOM    302  C   LEU A  18       1.767   2.212   1.044  1.00  0.00      A    C  
+ATOM    303  O   LEU A  18       2.276   1.320   0.421  1.00  0.00      A    O  
+ATOM    304  CB  LEU A  18      -0.707   2.750   1.156  1.00  0.00      A    C  
+ATOM    305  CG  LEU A  18      -0.799   2.763  -0.367  1.00  0.00      A    C  
+ATOM    306  CD1 LEU A  18      -1.004   1.321  -0.879  1.00  0.00      A    C  
+ATOM    307  CD2 LEU A  18      -1.835   3.808  -0.914  1.00  0.00      A    C  
+ATOM    308  H   LEU A  18      -0.098   3.338   3.350  1.00  0.00      A    H  
+ATOM    309  HA  LEU A  18       0.217   0.944   1.790  1.00  0.00      A    H  
+ATOM    310  HB2 LEU A  18      -1.672   2.466   1.576  1.00  0.00      A    H  
+ATOM    311  HB3 LEU A  18      -0.481   3.782   1.422  1.00  0.00      A    H  
+ATOM    312  HG  LEU A  18       0.198   3.047  -0.704  1.00  0.00      A    H  
+ATOM    313 HD11 LEU A  18      -0.033   0.926  -0.581  1.00  0.00      A    H  
+ATOM    314 HD12 LEU A  18      -1.142   1.369  -1.959  1.00  0.00      A    H  
+ATOM    315 HD13 LEU A  18      -1.873   0.844  -0.426  1.00  0.00      A    H  
+ATOM    316 HD21 LEU A  18      -1.338   4.368  -1.706  1.00  0.00      A    H  
+ATOM    317 HD22 LEU A  18      -2.148   4.594  -0.228  1.00  0.00      A    H  
+ATOM    318 HD23 LEU A  18      -2.737   3.274  -1.216  1.00  0.00      A    H  
+ATOM    319  N   ARG A  19       2.422   3.382   1.251  1.00  0.00      A    N  
+ATOM    320  CA  ARG A  19       3.770   3.733   0.499  1.00  0.00      A    C  
+ATOM    321  C   ARG A  19       4.978   2.933   1.078  1.00  0.00      A    C  
+ATOM    322  O   ARG A  19       5.931   2.658   0.432  1.00  0.00      A    O  
+ATOM    323  CB  ARG A  19       3.954   5.253   0.461  1.00  0.00      A    C  
+ATOM    324  CG  ARG A  19       2.835   5.968  -0.375  1.00  0.00      A    C  
+ATOM    325  CD  ARG A  19       3.107   5.890  -1.858  1.00  0.00      A    C  
+ATOM    326  NE  ARG A  19       1.893   6.010  -2.647  1.00  0.00      A    N  
+ATOM    327  CZ  ARG A  19       1.951   5.962  -4.011  1.00  0.00      A    C  
+ATOM    328  NH1 ARG A  19       3.092   6.091  -4.675  1.00  0.00      A    N  
+ATOM    329  NH2 ARG A  19       0.879   5.883  -4.711  1.00  0.00      A    N  
+ATOM    330  H   ARG A  19       2.050   4.061   1.900  1.00  0.00      A    H  
+ATOM    331  HA  ARG A  19       3.708   3.493  -0.562  1.00  0.00      A    H  
+ATOM    332  HB2 ARG A  19       3.937   5.594   1.497  1.00  0.00      A    H  
+ATOM    333  HB3 ARG A  19       4.893   5.392  -0.075  1.00  0.00      A    H  
+ATOM    334  HG2 ARG A  19       1.784   5.687  -0.303  1.00  0.00      A    H  
+ATOM    335  HG3 ARG A  19       2.858   7.032  -0.140  1.00  0.00      A    H  
+ATOM    336  HD2 ARG A  19       3.786   6.707  -2.102  1.00  0.00      A    H  
+ATOM    337  HD3 ARG A  19       3.490   4.888  -2.055  1.00  0.00      A    H  
+ATOM    338  HE  ARG A  19       1.000   5.938  -2.180  1.00  0.00      A    H  
+ATOM    339 HH11 ARG A  19       3.984   6.027  -4.205  1.00  0.00      A    H  
+ATOM    340 HH12 ARG A  19       3.104   6.010  -5.682  1.00  0.00      A    H  
+ATOM    341 HH21 ARG A  19       0.078   5.684  -4.129  1.00  0.00      A    H  
+ATOM    342 HH22 ARG A  19       0.926   5.795  -5.716  1.00  0.00      A    H  
+ATOM    343  N   ASP A  20       4.835   2.438   2.272  1.00  0.00      A    N  
+ATOM    344  CA  ASP A  20       5.679   1.376   2.746  1.00  0.00      A    C  
+ATOM    345  C   ASP A  20       5.619   0.041   1.907  1.00  0.00      A    C  
+ATOM    346  O   ASP A  20       6.550  -0.846   1.885  1.00  0.00      A    O  
+ATOM    347  CB  ASP A  20       5.413   1.103   4.233  1.00  0.00      A    C  
+ATOM    348  CG  ASP A  20       6.365   0.212   4.931  1.00  0.00      A    C  
+ATOM    349  OD1 ASP A  20       7.577   0.532   4.695  1.00  0.00      A    O  
+ATOM    350  OD2 ASP A  20       5.846  -0.665   5.673  1.00  0.00      A    O  
+ATOM    351  H   ASP A  20       4.048   2.776   2.808  1.00  0.00      A    H  
+ATOM    352  HA  ASP A  20       6.664   1.819   2.600  1.00  0.00      A    H  
+ATOM    353  HB2 ASP A  20       5.312   2.049   4.765  1.00  0.00      A    H  
+ATOM    354  HB3 ASP A  20       4.417   0.664   4.176  1.00  0.00      A    H  
+ATOM    355  N   PHE A  21       4.510  -0.142   1.117  1.00  0.00      A    N  
+ATOM    356  CA  PHE A  21       4.479  -1.362   0.191  1.00  0.00      A    C  
+ATOM    357  C   PHE A  21       4.967  -1.038  -1.187  1.00  0.00      A    C  
+ATOM    358  O   PHE A  21       5.796  -1.770  -1.680  1.00  0.00      A    O  
+ATOM    359  CB  PHE A  21       3.071  -1.941   0.316  1.00  0.00      A    C  
+ATOM    360  CG  PHE A  21       2.872  -3.128  -0.633  1.00  0.00      A    C  
+ATOM    361  CD1 PHE A  21       3.152  -4.479  -0.231  1.00  0.00      A    C  
+ATOM    362  CD2 PHE A  21       2.384  -2.961  -1.928  1.00  0.00      A    C  
+ATOM    363  CE1 PHE A  21       3.036  -5.521  -1.170  1.00  0.00      A    C  
+ATOM    364  CE2 PHE A  21       2.295  -3.938  -2.901  1.00  0.00      A    C  
+ATOM    365  CZ  PHE A  21       2.661  -5.203  -2.489  1.00  0.00      A    C  
+ATOM    366  H   PHE A  21       3.725   0.489   1.190  1.00  0.00      A    H  
+ATOM    367  HA  PHE A  21       5.159  -2.153   0.508  1.00  0.00      A    H  
+ATOM    368  HB2 PHE A  21       2.891  -2.337   1.316  1.00  0.00      A    H  
+ATOM    369  HB3 PHE A  21       2.317  -1.233  -0.026  1.00  0.00      A    H  
+ATOM    370  HD1 PHE A  21       3.483  -4.535   0.796  1.00  0.00      A    H  
+ATOM    371  HD2 PHE A  21       2.046  -1.959  -2.146  1.00  0.00      A    H  
+ATOM    372  HE1 PHE A  21       3.538  -6.450  -0.944  1.00  0.00      A    H  
+ATOM    373  HE2 PHE A  21       2.014  -3.675  -3.911  1.00  0.00      A    H  
+ATOM    374  HZ  PHE A  21       2.789  -5.988  -3.220  1.00  0.00      A    H  
+ATOM    375  N   ILE A  22       4.493   0.047  -1.893  1.00  0.00      A    N  
+ATOM    376  CA  ILE A  22       4.911   0.267  -3.300  1.00  0.00      A    C  
+ATOM    377  C   ILE A  22       6.442   0.524  -3.333  1.00  0.00      A    C  
+ATOM    378  O   ILE A  22       7.124  -0.083  -4.178  1.00  0.00      A    O  
+ATOM    379  CB  ILE A  22       4.016   1.326  -4.011  1.00  0.00      A    C  
+ATOM    380  CG1 ILE A  22       2.615   0.855  -4.450  1.00  0.00      A    C  
+ATOM    381  CG2 ILE A  22       4.773   2.057  -5.141  1.00  0.00      A    C  
+ATOM    382  CD1 ILE A  22       1.566   1.000  -3.308  1.00  0.00      A    C  
+ATOM    383  H   ILE A  22       3.777   0.577  -1.416  1.00  0.00      A    H  
+ATOM    384  HA  ILE A  22       4.551  -0.571  -3.897  1.00  0.00      A    H  
+ATOM    385  HB  ILE A  22       3.752   2.148  -3.347  1.00  0.00      A    H  
+ATOM    386 HG12 ILE A  22       2.246   1.515  -5.235  1.00  0.00      A    H  
+ATOM    387 HG13 ILE A  22       2.579  -0.172  -4.814  1.00  0.00      A    H  
+ATOM    388 HG21 ILE A  22       4.033   2.677  -5.647  1.00  0.00      A    H  
+ATOM    389 HG22 ILE A  22       5.307   1.382  -5.810  1.00  0.00      A    H  
+ATOM    390 HG23 ILE A  22       5.468   2.787  -4.726  1.00  0.00      A    H  
+ATOM    391 HD11 ILE A  22       1.897   0.404  -2.457  1.00  0.00      A    H  
+ATOM    392 HD12 ILE A  22       0.620   0.493  -3.499  1.00  0.00      A    H  
+ATOM    393 HD13 ILE A  22       1.307   2.009  -2.987  1.00  0.00      A    H  
+ATOM    394  N   GLU A  23       7.067   1.237  -2.397  1.00  0.00      A    N  
+ATOM    395  CA  GLU A  23       8.512   1.285  -2.234  1.00  0.00      A    C  
+ATOM    396  C   GLU A  23       9.374  -0.002  -2.186  1.00  0.00      A    C  
+ATOM    397  O   GLU A  23      10.548  -0.111  -2.515  1.00  0.00      A    O  
+ATOM    398  CB  GLU A  23       8.811   2.330  -1.173  1.00  0.00      A    C  
+ATOM    399  CG  GLU A  23      10.254   2.888  -1.081  1.00  0.00      A    C  
+ATOM    400  CD  GLU A  23      10.443   4.061  -0.186  1.00  0.00      A    C  
+ATOM    401  OE1 GLU A  23      11.199   4.018   0.799  1.00  0.00      A    O  
+ATOM    402  OE2 GLU A  23       9.830   5.117  -0.492  1.00  0.00      A    O  
+ATOM    403  H   GLU A  23       6.562   1.819  -1.743  1.00  0.00      A    H  
+ATOM    404  HA  GLU A  23       8.859   1.795  -3.132  1.00  0.00      A    H  
+ATOM    405  HB2 GLU A  23       8.128   3.169  -1.304  1.00  0.00      A    H  
+ATOM    406  HB3 GLU A  23       8.512   1.974  -0.187  1.00  0.00      A    H  
+ATOM    407  HG2 GLU A  23      10.995   2.110  -0.895  1.00  0.00      A    H  
+ATOM    408  HG3 GLU A  23      10.418   3.161  -2.124  1.00  0.00      A    H  
+ATOM    409  N   LYS A  24       8.716  -1.118  -1.887  1.00  0.00      A    N  
+ATOM    410  CA  LYS A  24       9.307  -2.472  -1.874  1.00  0.00      A    C  
+ATOM    411  C   LYS A  24       8.858  -3.329  -3.086  1.00  0.00      A    C  
+ATOM    412  O   LYS A  24       9.665  -4.104  -3.644  1.00  0.00      A    O  
+ATOM    413  CB  LYS A  24       9.073  -3.198  -0.469  1.00  0.00      A    C  
+ATOM    414  CG  LYS A  24       9.830  -2.469   0.690  1.00  0.00      A    C  
+ATOM    415  CD  LYS A  24      11.303  -2.850   0.841  1.00  0.00      A    C  
+ATOM    416  CE  LYS A  24      12.061  -2.141   2.008  1.00  0.00      A    C  
+ATOM    417  NZ  LYS A  24      11.452  -2.599   3.307  1.00  0.00      A    N  
+ATOM    418  H   LYS A  24       7.733  -1.031  -1.672  1.00  0.00      A    H  
+ATOM    419  HA  LYS A  24      10.389  -2.446  -2.009  1.00  0.00      A    H  
+ATOM    420  HB2 LYS A  24       8.002  -3.033  -0.348  1.00  0.00      A    H  
+ATOM    421  HB3 LYS A  24       9.395  -4.233  -0.588  1.00  0.00      A    H  
+ATOM    422  HG2 LYS A  24       9.567  -1.416   0.589  1.00  0.00      A    H  
+ATOM    423  HG3 LYS A  24       9.374  -2.875   1.593  1.00  0.00      A    H  
+ATOM    424  HD2 LYS A  24      11.409  -3.931   0.939  1.00  0.00      A    H  
+ATOM    425  HD3 LYS A  24      11.856  -2.581  -0.059  1.00  0.00      A    H  
+ATOM    426  HE2 LYS A  24      13.147  -2.237   1.986  1.00  0.00      A    H  
+ATOM    427  HE3 LYS A  24      11.949  -1.075   1.809  1.00  0.00      A    H  
+ATOM    428  HZ1 LYS A  24      10.512  -2.299   3.525  1.00  0.00      A    H  
+ATOM    429  HZ2 LYS A  24      12.017  -2.492   4.137  1.00  0.00      A    H  
+ATOM    430  HZ3 LYS A  24      11.359  -3.599   3.416  1.00  0.00      A    H  
+ATOM    431  N   PHE A  25       7.631  -3.061  -3.583  1.00  0.00      A    N  
+ATOM    432  CA  PHE A  25       7.036  -3.461  -4.870  1.00  0.00      A    C  
+ATOM    433  C   PHE A  25       7.940  -3.117  -6.155  1.00  0.00      A    C  
+ATOM    434  O   PHE A  25       7.622  -3.533  -7.253  1.00  0.00      A    O  
+ATOM    435  CB  PHE A  25       5.657  -2.871  -5.023  1.00  0.00      A    C  
+ATOM    436  CG  PHE A  25       4.781  -3.650  -6.012  1.00  0.00      A    C  
+ATOM    437  CD1 PHE A  25       4.199  -4.877  -5.645  1.00  0.00      A    C  
+ATOM    438  CD2 PHE A  25       4.481  -3.065  -7.285  1.00  0.00      A    C  
+ATOM    439  CE1 PHE A  25       3.380  -5.659  -6.590  1.00  0.00      A    C  
+ATOM    440  CE2 PHE A  25       3.597  -3.836  -8.140  1.00  0.00      A    C  
+ATOM    441  CZ  PHE A  25       2.997  -5.044  -7.830  1.00  0.00      A    C  
+ATOM    442  H   PHE A  25       7.050  -2.522  -2.957  1.00  0.00      A    H  
+ATOM    443  HA  PHE A  25       7.029  -4.551  -4.855  1.00  0.00      A    H  
+ATOM    444  HB2 PHE A  25       5.082  -3.041  -4.113  1.00  0.00      A    H  
+ATOM    445  HB3 PHE A  25       5.776  -1.847  -5.378  1.00  0.00      A    H  
+ATOM    446  HD1 PHE A  25       4.420  -5.231  -4.649  1.00  0.00      A    H  
+ATOM    447  HD2 PHE A  25       4.874  -2.107  -7.591  1.00  0.00      A    H  
+ATOM    448  HE1 PHE A  25       2.813  -6.539  -6.327  1.00  0.00      A    H  
+ATOM    449  HE2 PHE A  25       3.283  -3.319  -9.035  1.00  0.00      A    H  
+ATOM    450  HZ  PHE A  25       2.300  -5.603  -8.437  1.00  0.00      A    H  
+ATOM    451  N   LYS A  26       9.030  -2.366  -6.002  1.00  0.00      A    N  
+ATOM    452  CA  LYS A  26      10.067  -2.124  -6.967  1.00  0.00      A    C  
+ATOM    453  C   LYS A  26      11.129  -3.241  -7.079  1.00  0.00      A    C  
+ATOM    454  O   LYS A  26      11.745  -3.441  -8.185  1.00  0.00      A    O  
+ATOM    455  CB  LYS A  26      10.618  -0.753  -6.504  1.00  0.00      A    C  
+ATOM    456  CG  LYS A  26       9.693   0.438  -6.750  1.00  0.00      A    C  
+ATOM    457  CD  LYS A  26      10.065   1.715  -6.017  1.00  0.00      A    C  
+ATOM    458  CE  LYS A  26      11.430   2.205  -6.517  1.00  0.00      A    C  
+ATOM    459  NZ  LYS A  26      12.043   3.155  -5.520  1.00  0.00      A    N  
+ATOM    460  H   LYS A  26       9.147  -1.928  -5.099  1.00  0.00      A    H  
+ATOM    461  HA  LYS A  26       9.703  -2.030  -7.991  1.00  0.00      A    H  
+ATOM    462  HB2 LYS A  26      10.826  -0.859  -5.439  1.00  0.00      A    H  
+ATOM    463  HB3 LYS A  26      11.552  -0.622  -7.050  1.00  0.00      A    H  
+ATOM    464  HG2 LYS A  26       9.671   0.698  -7.809  1.00  0.00      A    H  
+ATOM    465  HG3 LYS A  26       8.660   0.301  -6.432  1.00  0.00      A    H  
+ATOM    466  HD2 LYS A  26       9.318   2.426  -6.370  1.00  0.00      A    H  
+ATOM    467  HD3 LYS A  26      10.157   1.492  -4.954  1.00  0.00      A    H  
+ATOM    468  HE2 LYS A  26      12.070   1.327  -6.599  1.00  0.00      A    H  
+ATOM    469  HE3 LYS A  26      11.355   2.749  -7.459  1.00  0.00      A    H  
+ATOM    470  HZ1 LYS A  26      12.342   2.742  -4.648  1.00  0.00      A    H  
+ATOM    471  HZ2 LYS A  26      11.419   3.882  -5.202  1.00  0.00      A    H  
+ATOM    472  HZ3 LYS A  26      12.951   3.437  -5.861  1.00  0.00      A    H  
+ATOM    473  N   GLY A  27      11.203  -4.185  -6.135  1.00  0.00      A    N  
+ATOM    474  CA  GLY A  27      12.245  -5.277  -6.200  1.00  0.00      A    C  
+ATOM    475  C   GLY A  27      12.303  -6.417  -5.189  1.00  0.00      A    C  
+ATOM    476  O   GLY A  27      13.024  -7.384  -5.358  1.00  0.00      A    O  
+ATOM    477  H   GLY A  27      10.572  -4.023  -5.363  1.00  0.00      A    H  
+ATOM    478  HA2 GLY A  27      12.295  -5.727  -7.192  1.00  0.00      A    H  
+ATOM    479  HA3 GLY A  27      13.193  -4.757  -6.061  1.00  0.00      A    H  
+ATOM    480  N   ARG A  28      11.648  -6.204  -4.050  1.00  0.00      A    N  
+ATOM    481  CA  ARG A  28      11.843  -7.016  -2.825  1.00  0.00      A    C  
+ATOM    482  C   ARG A  28      10.465  -7.599  -2.428  1.00  0.00      A    C  
+ATOM    483  O   ARG A  28      10.160  -8.653  -2.968  1.00  0.00      A    O  
+ATOM    484  CB  ARG A  28      12.567  -6.206  -1.682  1.00  0.00      A    C  
+ATOM    485  CG  ARG A  28      13.954  -5.592  -2.164  1.00  0.00      A    C  
+ATOM    486  CD  ARG A  28      14.538  -4.936  -0.890  1.00  0.00      A    C  
+ATOM    487  NE  ARG A  28      15.927  -4.408  -1.136  1.00  0.00      A    N  
+ATOM    488  CZ  ARG A  28      16.724  -4.142  -0.141  1.00  0.00      A    C  
+ATOM    489  NH1 ARG A  28      16.380  -4.268   1.109  1.00  0.00      A    N  
+ATOM    490  NH2 ARG A  28      17.962  -3.672  -0.292  1.00  0.00      A    N  
+ATOM    491  OXT ARG A  28       9.747  -6.925  -1.642  1.00  0.00      A    O  
+ATOM    492  H   ARG A  28      10.981  -5.447  -3.997  1.00  0.00      A    H  
+ATOM    493  HA  ARG A  28      12.497  -7.867  -3.014  1.00  0.00      A    H  
+ATOM    494  HB2 ARG A  28      12.056  -5.335  -1.273  1.00  0.00      A    H  
+ATOM    495  HB3 ARG A  28      12.791  -6.866  -0.844  1.00  0.00      A    H  
+ATOM    496  HG2 ARG A  28      14.701  -6.230  -2.637  1.00  0.00      A    H  
+ATOM    497  HG3 ARG A  28      13.832  -4.925  -3.018  1.00  0.00      A    H  
+ATOM    498  HD2 ARG A  28      13.823  -4.164  -0.604  1.00  0.00      A    H  
+ATOM    499  HD3 ARG A  28      14.614  -5.683  -0.101  1.00  0.00      A    H  
+ATOM    500  HE  ARG A  28      16.342  -4.209  -2.034  1.00  0.00      A    H  
+ATOM    501 HH11 ARG A  28      15.404  -4.360   1.353  1.00  0.00      A    H  
+ATOM    502 HH12 ARG A  28      16.964  -4.032   1.898  1.00  0.00      A    H  
+ATOM    503 HH21 ARG A  28      18.400  -3.645  -1.202  1.00  0.00      A    H  
+ATOM    504 HH22 ARG A  28      18.411  -3.259   0.513  1.00  0.00      A    H  
+ENDMDL
+END

entangled-tps/data/bba/path.gro

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3f07c5e9042d5003e8e048906a985710890828878bdda913315c51b66007a313
+size 54665982

entangled-tps/data/bba/tica_model.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:77300123d261710b6f17bcfac5a870b4d42915cf57abcf29ce3f0dc74fd70086
+size 752721

entangled-tps/data/bba/unfolded.pdb

@@ -0,0 +1,515 @@
+TITLE     MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter
+CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1           1
+REMARK     285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET
+REMARK     285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION
+REMARK     285 WAS MISSING.
+REMARK     285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
+REMARK     285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON
+REMARK     285 THIS RECORD ARE MEANINGLESS.
+MODEL        1
+ATOM      1  N   GLU A   1     -13.633  -2.853  19.490  1.00  0.00      A    N  
+ATOM      2  CA  GLU A   1     -13.212  -4.007  18.774  1.00  0.00      A    C  
+ATOM      3  C   GLU A   1     -12.455  -3.550  17.505  1.00  0.00      A    C  
+ATOM      4  O   GLU A   1     -13.076  -2.780  16.738  1.00  0.00      A    O  
+ATOM      5  CB  GLU A   1     -14.368  -4.905  18.207  1.00  0.00      A    C  
+ATOM      6  CG  GLU A   1     -13.894  -6.135  17.353  1.00  0.00      A    C  
+ATOM      7  CD  GLU A   1     -12.876  -7.030  18.099  1.00  0.00      A    C  
+ATOM      8  OE1 GLU A   1     -11.814  -6.566  18.548  1.00  0.00      A    O  
+ATOM      9  OE2 GLU A   1     -13.142  -8.261  18.082  1.00  0.00      A    O  
+ATOM     10  H1  GLU A   1     -14.494  -3.083  19.965  1.00  0.00      A    H  
+ATOM     11  H2  GLU A   1     -13.848  -2.043  18.926  1.00  0.00      A    H  
+ATOM     12  H3  GLU A   1     -13.027  -2.436  20.182  1.00  0.00      A    H  
+ATOM     13  HA  GLU A   1     -12.564  -4.674  19.342  1.00  0.00      A    H  
+ATOM     14  HB2 GLU A   1     -15.163  -5.241  18.873  1.00  0.00      A    H  
+ATOM     15  HB3 GLU A   1     -15.002  -4.403  17.477  1.00  0.00      A    H  
+ATOM     16  HG2 GLU A   1     -14.597  -6.824  16.884  1.00  0.00      A    H  
+ATOM     17  HG3 GLU A   1     -13.525  -5.630  16.460  1.00  0.00      A    H  
+ATOM     18  N   GLN A   2     -11.247  -3.979  17.294  1.00  0.00      A    N  
+ATOM     19  CA  GLN A   2     -10.494  -3.860  15.959  1.00  0.00      A    C  
+ATOM     20  C   GLN A   2      -9.369  -4.984  16.005  1.00  0.00      A    C  
+ATOM     21  O   GLN A   2      -8.362  -4.859  16.662  1.00  0.00      A    O  
+ATOM     22  CB  GLN A   2      -9.817  -2.523  15.667  1.00  0.00      A    C  
+ATOM     23  CG  GLN A   2      -9.523  -1.769  17.007  1.00  0.00      A    C  
+ATOM     24  CD  GLN A   2      -8.229  -1.020  16.883  1.00  0.00      A    C  
+ATOM     25  OE1 GLN A   2      -7.799  -0.600  15.815  1.00  0.00      A    O  
+ATOM     26  NE2 GLN A   2      -7.511  -0.906  17.984  1.00  0.00      A    N  
+ATOM     27  H   GLN A   2     -10.956  -4.692  17.948  1.00  0.00      A    H  
+ATOM     28  HA  GLN A   2     -11.027  -4.047  15.027  1.00  0.00      A    H  
+ATOM     29  HB2 GLN A   2      -8.867  -2.618  15.140  1.00  0.00      A    H  
+ATOM     30  HB3 GLN A   2     -10.390  -1.837  15.044  1.00  0.00      A    H  
+ATOM     31  HG2 GLN A   2     -10.253  -0.973  17.154  1.00  0.00      A    H  
+ATOM     32  HG3 GLN A   2      -9.336  -2.436  17.849  1.00  0.00      A    H  
+ATOM     33 HE21 GLN A   2      -7.875  -1.262  18.857  1.00  0.00      A    H  
+ATOM     34 HE22 GLN A   2      -6.560  -0.567  17.976  1.00  0.00      A    H  
+ATOM     35  N   TYR A   3      -9.483  -6.042  15.223  1.00  0.00      A    N  
+ATOM     36  CA  TYR A   3      -8.492  -7.069  14.903  1.00  0.00      A    C  
+ATOM     37  C   TYR A   3      -7.319  -6.536  14.091  1.00  0.00      A    C  
+ATOM     38  O   TYR A   3      -7.462  -5.699  13.232  1.00  0.00      A    O  
+ATOM     39  CB  TYR A   3      -9.209  -8.220  14.296  1.00  0.00      A    C  
+ATOM     40  CG  TYR A   3      -8.361  -9.385  13.806  1.00  0.00      A    C  
+ATOM     41  CD1 TYR A   3      -7.796 -10.370  14.703  1.00  0.00      A    C  
+ATOM     42  CD2 TYR A   3      -7.949  -9.431  12.398  1.00  0.00      A    C  
+ATOM     43  CE1 TYR A   3      -6.900 -11.325  14.248  1.00  0.00      A    C  
+ATOM     44  CE2 TYR A   3      -7.124 -10.494  11.994  1.00  0.00      A    C  
+ATOM     45  CZ  TYR A   3      -6.569 -11.420  12.882  1.00  0.00      A    C  
+ATOM     46  OH  TYR A   3      -5.918 -12.529  12.412  1.00  0.00      A    O  
+ATOM     47  H   TYR A   3     -10.275  -6.015  14.598  1.00  0.00      A    H  
+ATOM     48  HA  TYR A   3      -8.104  -7.383  15.872  1.00  0.00      A    H  
+ATOM     49  HB2 TYR A   3      -9.994  -8.574  14.963  1.00  0.00      A    H  
+ATOM     50  HB3 TYR A   3      -9.709  -7.818  13.415  1.00  0.00      A    H  
+ATOM     51  HD1 TYR A   3      -8.085 -10.424  15.742  1.00  0.00      A    H  
+ATOM     52  HD2 TYR A   3      -8.372  -8.850  11.592  1.00  0.00      A    H  
+ATOM     53  HE1 TYR A   3      -6.677 -12.137  14.924  1.00  0.00      A    H  
+ATOM     54  HE2 TYR A   3      -6.744 -10.620  10.991  1.00  0.00      A    H  
+ATOM     55  HH  TYR A   3      -6.014 -13.272  13.013  1.00  0.00      A    H  
+ATOM     56  N   THR A   4      -6.059  -7.005  14.416  1.00  0.00      A    N  
+ATOM     57  CA  THR A   4      -4.738  -6.486  13.888  1.00  0.00      A    C  
+ATOM     58  C   THR A   4      -3.781  -7.570  13.262  1.00  0.00      A    C  
+ATOM     59  O   THR A   4      -3.626  -8.639  13.868  1.00  0.00      A    O  
+ATOM     60  CB  THR A   4      -4.195  -5.449  14.893  1.00  0.00      A    C  
+ATOM     61  OG1 THR A   4      -3.150  -4.640  14.443  1.00  0.00      A    O  
+ATOM     62  CG2 THR A   4      -3.666  -6.106  16.098  1.00  0.00      A    C  
+ATOM     63  H   THR A   4      -6.027  -7.762  15.084  1.00  0.00      A    H  
+ATOM     64  HA  THR A   4      -5.004  -5.847  13.046  1.00  0.00      A    H  
+ATOM     65  HB  THR A   4      -5.036  -4.790  15.106  1.00  0.00      A    H  
+ATOM     66  HG1 THR A   4      -3.366  -3.726  14.244  1.00  0.00      A    H  
+ATOM     67 HG21 THR A   4      -2.994  -6.892  15.755  1.00  0.00      A    H  
+ATOM     68 HG22 THR A   4      -4.469  -6.683  16.558  1.00  0.00      A    H  
+ATOM     69 HG23 THR A   4      -3.303  -5.373  16.819  1.00  0.00      A    H  
+ATOM     70  N   ALA A   5      -3.166  -7.269  12.148  1.00  0.00      A    N  
+ATOM     71  CA  ALA A   5      -2.082  -7.988  11.483  1.00  0.00      A    C  
+ATOM     72  C   ALA A   5      -0.865  -7.328  10.731  1.00  0.00      A    C  
+ATOM     73  O   ALA A   5      -0.028  -8.017  10.139  1.00  0.00      A    O  
+ATOM     74  CB  ALA A   5      -2.749  -8.921  10.386  1.00  0.00      A    C  
+ATOM     75  H   ALA A   5      -3.562  -6.444  11.721  1.00  0.00      A    H  
+ATOM     76  HA  ALA A   5      -1.725  -8.723  12.205  1.00  0.00      A    H  
+ATOM     77  HB1 ALA A   5      -3.084  -8.323   9.539  1.00  0.00      A    H  
+ATOM     78  HB2 ALA A   5      -3.585  -9.488  10.795  1.00  0.00      A    H  
+ATOM     79  HB3 ALA A   5      -2.124  -9.658   9.881  1.00  0.00      A    H  
+ATOM     80  N   LYS A   6      -0.760  -5.974  10.739  1.00  0.00      A    N  
+ATOM     81  CA  LYS A   6       0.228  -5.135  10.021  1.00  0.00      A    C  
+ATOM     82  C   LYS A   6       1.686  -5.395  10.414  1.00  0.00      A    C  
+ATOM     83  O   LYS A   6       2.588  -4.834   9.705  1.00  0.00      A    O  
+ATOM     84  CB  LYS A   6      -0.175  -3.688  10.226  1.00  0.00      A    C  
+ATOM     85  CG  LYS A   6       0.023  -3.275  11.760  1.00  0.00      A    C  
+ATOM     86  CD  LYS A   6      -0.109  -1.769  11.725  1.00  0.00      A    C  
+ATOM     87  CE  LYS A   6      -0.104  -1.142  13.177  1.00  0.00      A    C  
+ATOM     88  NZ  LYS A   6       0.038   0.266  12.979  1.00  0.00      A    N  
+ATOM     89  H   LYS A   6      -1.368  -5.515  11.402  1.00  0.00      A    H  
+ATOM     90  HA  LYS A   6       0.067  -5.302   8.956  1.00  0.00      A    H  
+ATOM     91  HB2 LYS A   6       0.488  -3.136   9.559  1.00  0.00      A    H  
+ATOM     92  HB3 LYS A   6      -1.196  -3.502   9.894  1.00  0.00      A    H  
+ATOM     93  HG2 LYS A   6      -0.823  -3.699  12.300  1.00  0.00      A    H  
+ATOM     94  HG3 LYS A   6       0.953  -3.792  11.997  1.00  0.00      A    H  
+ATOM     95  HD2 LYS A   6       0.851  -1.540  11.263  1.00  0.00      A    H  
+ATOM     96  HD3 LYS A   6      -1.021  -1.579  11.159  1.00  0.00      A    H  
+ATOM     97  HE2 LYS A   6      -0.988  -1.361  13.775  1.00  0.00      A    H  
+ATOM     98  HE3 LYS A   6       0.815  -1.502  13.639  1.00  0.00      A    H  
+ATOM     99  HZ1 LYS A   6      -0.084   0.786  13.836  1.00  0.00      A    H  
+ATOM    100  HZ2 LYS A   6      -0.728   0.445  12.346  1.00  0.00      A    H  
+ATOM    101  HZ3 LYS A   6       0.852   0.594  12.480  1.00  0.00      A    H  
+ATOM    102  N   TYR A   7       1.911  -6.198  11.490  1.00  0.00      A    N  
+ATOM    103  CA  TYR A   7       3.305  -6.711  11.680  1.00  0.00      A    C  
+ATOM    104  C   TYR A   7       3.668  -8.089  11.074  1.00  0.00      A    C  
+ATOM    105  O   TYR A   7       4.884  -8.407  11.052  1.00  0.00      A    O  
+ATOM    106  CB  TYR A   7       3.543  -6.737  13.131  1.00  0.00      A    C  
+ATOM    107  CG  TYR A   7       2.420  -7.391  14.012  1.00  0.00      A    C  
+ATOM    108  CD1 TYR A   7       1.273  -6.655  14.496  1.00  0.00      A    C  
+ATOM    109  CD2 TYR A   7       2.460  -8.740  14.287  1.00  0.00      A    C  
+ATOM    110  CE1 TYR A   7       0.164  -7.345  15.044  1.00  0.00      A    C  
+ATOM    111  CE2 TYR A   7       1.457  -9.485  14.938  1.00  0.00      A    C  
+ATOM    112  CZ  TYR A   7       0.254  -8.790  15.286  1.00  0.00      A    C  
+ATOM    113  OH  TYR A   7      -0.767  -9.471  15.805  1.00  0.00      A    O  
+ATOM    114  H   TYR A   7       1.214  -6.556  12.126  1.00  0.00      A    H  
+ATOM    115  HA  TYR A   7       4.029  -6.022  11.245  1.00  0.00      A    H  
+ATOM    116  HB2 TYR A   7       4.508  -7.212  13.304  1.00  0.00      A    H  
+ATOM    117  HB3 TYR A   7       3.645  -5.661  13.274  1.00  0.00      A    H  
+ATOM    118  HD1 TYR A   7       1.221  -5.593  14.306  1.00  0.00      A    H  
+ATOM    119  HD2 TYR A   7       3.306  -9.319  13.948  1.00  0.00      A    H  
+ATOM    120  HE1 TYR A   7      -0.642  -6.738  15.430  1.00  0.00      A    H  
+ATOM    121  HE2 TYR A   7       1.435 -10.545  15.143  1.00  0.00      A    H  
+ATOM    122  HH  TYR A   7      -1.596  -9.222  15.390  1.00  0.00      A    H  
+ATOM    123  N   LYS A   8       2.694  -8.910  10.611  1.00  0.00      A    N  
+ATOM    124  CA  LYS A   8       2.808 -10.230   9.950  1.00  0.00      A    C  
+ATOM    125  C   LYS A   8       2.483 -10.115   8.436  1.00  0.00      A    C  
+ATOM    126  O   LYS A   8       3.013 -10.904   7.668  1.00  0.00      A    O  
+ATOM    127  CB  LYS A   8       2.089 -11.230  10.836  1.00  0.00      A    C  
+ATOM    128  CG  LYS A   8       0.615 -11.492  10.334  1.00  0.00      A    C  
+ATOM    129  CD  LYS A   8       0.384 -12.396   9.095  1.00  0.00      A    C  
+ATOM    130  CE  LYS A   8      -1.100 -12.587   8.906  1.00  0.00      A    C  
+ATOM    131  NZ  LYS A   8      -1.563 -14.009   8.949  1.00  0.00      A    N  
+ATOM    132  H   LYS A   8       1.813  -8.422  10.674  1.00  0.00      A    H  
+ATOM    133  HA  LYS A   8       3.840 -10.581   9.947  1.00  0.00      A    H  
+ATOM    134  HB2 LYS A   8       2.704 -12.125  10.741  1.00  0.00      A    H  
+ATOM    135  HB3 LYS A   8       2.078 -10.882  11.869  1.00  0.00      A    H  
+ATOM    136  HG2 LYS A   8      -0.004 -11.813  11.172  1.00  0.00      A    H  
+ATOM    137  HG3 LYS A   8       0.270 -10.494  10.062  1.00  0.00      A    H  
+ATOM    138  HD2 LYS A   8       0.668 -11.906   8.164  1.00  0.00      A    H  
+ATOM    139  HD3 LYS A   8       0.872 -13.369   9.158  1.00  0.00      A    H  
+ATOM    140  HE2 LYS A   8      -1.543 -11.982   9.696  1.00  0.00      A    H  
+ATOM    141  HE3 LYS A   8      -1.320 -12.236   7.898  1.00  0.00      A    H  
+ATOM    142  HZ1 LYS A   8      -2.567 -14.105   8.888  1.00  0.00      A    H  
+ATOM    143  HZ2 LYS A   8      -1.205 -14.398   9.810  1.00  0.00      A    H  
+ATOM    144  HZ3 LYS A   8      -1.217 -14.660   8.259  1.00  0.00      A    H  
+ATOM    145  N   GLY A   9       1.769  -9.052   8.014  1.00  0.00      A    N  
+ATOM    146  CA  GLY A   9       1.549  -8.661   6.583  1.00  0.00      A    C  
+ATOM    147  C   GLY A   9       0.797  -7.376   6.326  1.00  0.00      A    C  
+ATOM    148  O   GLY A   9       0.186  -6.811   7.216  1.00  0.00      A    O  
+ATOM    149  H   GLY A   9       1.276  -8.567   8.750  1.00  0.00      A    H  
+ATOM    150  HA2 GLY A   9       2.490  -8.606   6.036  1.00  0.00      A    H  
+ATOM    151  HA3 GLY A   9       0.886  -9.404   6.139  1.00  0.00      A    H  
+ATOM    152  N   ARG A  10       0.952  -6.808   5.112  1.00  0.00      A    N  
+ATOM    153  CA  ARG A  10       0.353  -5.523   4.617  1.00  0.00      A    C  
+ATOM    154  C   ARG A  10      -0.351  -5.444   3.186  1.00  0.00      A    C  
+ATOM    155  O   ARG A  10       0.246  -5.621   2.102  1.00  0.00      A    O  
+ATOM    156  CB  ARG A  10       1.400  -4.364   4.737  1.00  0.00      A    C  
+ATOM    157  CG  ARG A  10       1.855  -4.051   6.209  1.00  0.00      A    C  
+ATOM    158  CD  ARG A  10       2.907  -2.935   6.278  1.00  0.00      A    C  
+ATOM    159  NE  ARG A  10       3.583  -2.876   7.613  1.00  0.00      A    N  
+ATOM    160  CZ  ARG A  10       4.377  -1.973   8.131  1.00  0.00      A    C  
+ATOM    161  NH1 ARG A  10       4.682  -0.853   7.429  1.00  0.00      A    N  
+ATOM    162  NH2 ARG A  10       4.913  -2.129   9.280  1.00  0.00      A    N  
+ATOM    163  H   ARG A  10       1.392  -7.308   4.352  1.00  0.00      A    H  
+ATOM    164  HA  ARG A  10      -0.486  -5.310   5.279  1.00  0.00      A    H  
+ATOM    165  HB2 ARG A  10       2.222  -4.681   4.096  1.00  0.00      A    H  
+ATOM    166  HB3 ARG A  10       1.035  -3.394   4.400  1.00  0.00      A    H  
+ATOM    167  HG2 ARG A  10       0.923  -3.712   6.662  1.00  0.00      A    H  
+ATOM    168  HG3 ARG A  10       2.233  -4.867   6.825  1.00  0.00      A    H  
+ATOM    169  HD2 ARG A  10       3.720  -3.053   5.561  1.00  0.00      A    H  
+ATOM    170  HD3 ARG A  10       2.419  -1.980   6.083  1.00  0.00      A    H  
+ATOM    171  HE  ARG A  10       3.601  -3.778   8.068  1.00  0.00      A    H  
+ATOM    172 HH11 ARG A  10       4.332  -0.659   6.502  1.00  0.00      A    H  
+ATOM    173 HH12 ARG A  10       5.370  -0.276   7.891  1.00  0.00      A    H  
+ATOM    174 HH21 ARG A  10       4.787  -2.991   9.790  1.00  0.00      A    H  
+ATOM    175 HH22 ARG A  10       5.397  -1.356   9.714  1.00  0.00      A    H  
+ATOM    176  N   THR A  11      -1.649  -4.931   3.127  1.00  0.00      A    N  
+ATOM    177  CA  THR A  11      -2.163  -4.454   1.791  1.00  0.00      A    C  
+ATOM    178  C   THR A  11      -1.862  -2.932   1.606  1.00  0.00      A    C  
+ATOM    179  O   THR A  11      -1.386  -2.151   2.504  1.00  0.00      A    O  
+ATOM    180  CB  THR A  11      -3.618  -4.835   1.753  1.00  0.00      A    C  
+ATOM    181  OG1 THR A  11      -4.085  -4.652   0.417  1.00  0.00      A    O  
+ATOM    182  CG2 THR A  11      -4.535  -4.003   2.636  1.00  0.00      A    C  
+ATOM    183  H   THR A  11      -2.258  -4.717   3.904  1.00  0.00      A    H  
+ATOM    184  HA  THR A  11      -1.627  -4.933   0.972  1.00  0.00      A    H  
+ATOM    185  HB  THR A  11      -3.618  -5.887   2.039  1.00  0.00      A    H  
+ATOM    186  HG1 THR A  11      -4.979  -4.306   0.372  1.00  0.00      A    H  
+ATOM    187 HG21 THR A  11      -3.940  -3.481   3.385  1.00  0.00      A    H  
+ATOM    188 HG22 THR A  11      -5.295  -4.537   3.206  1.00  0.00      A    H  
+ATOM    189 HG23 THR A  11      -4.993  -3.241   2.005  1.00  0.00      A    H  
+ATOM    190  N   PHE A  12      -1.919  -2.665   0.269  1.00  0.00      A    N  
+ATOM    191  CA  PHE A  12      -1.365  -1.482  -0.469  1.00  0.00      A    C  
+ATOM    192  C   PHE A  12      -1.741  -0.160   0.044  1.00  0.00      A    C  
+ATOM    193  O   PHE A  12      -0.873   0.709   0.185  1.00  0.00      A    O  
+ATOM    194  CB  PHE A  12      -1.669  -1.633  -1.924  1.00  0.00      A    C  
+ATOM    195  CG  PHE A  12      -1.146  -2.945  -2.552  1.00  0.00      A    C  
+ATOM    196  CD1 PHE A  12       0.193  -3.217  -2.854  1.00  0.00      A    C  
+ATOM    197  CD2 PHE A  12      -2.112  -3.962  -2.956  1.00  0.00      A    C  
+ATOM    198  CE1 PHE A  12       0.583  -4.368  -3.548  1.00  0.00      A    C  
+ATOM    199  CE2 PHE A  12      -1.725  -5.095  -3.704  1.00  0.00      A    C  
+ATOM    200  CZ  PHE A  12      -0.370  -5.329  -4.018  1.00  0.00      A    C  
+ATOM    201  H   PHE A  12      -2.313  -3.413  -0.282  1.00  0.00      A    H  
+ATOM    202  HA  PHE A  12      -0.309  -1.680  -0.288  1.00  0.00      A    H  
+ATOM    203  HB2 PHE A  12      -2.750  -1.721  -2.031  1.00  0.00      A    H  
+ATOM    204  HB3 PHE A  12      -1.167  -0.814  -2.440  1.00  0.00      A    H  
+ATOM    205  HD1 PHE A  12       1.025  -2.538  -2.732  1.00  0.00      A    H  
+ATOM    206  HD2 PHE A  12      -3.119  -3.743  -2.633  1.00  0.00      A    H  
+ATOM    207  HE1 PHE A  12       1.640  -4.562  -3.652  1.00  0.00      A    H  
+ATOM    208  HE2 PHE A  12      -2.553  -5.722  -4.001  1.00  0.00      A    H  
+ATOM    209  HZ  PHE A  12       0.040  -6.218  -4.473  1.00  0.00      A    H  
+ATOM    210  N   ARG A  13      -3.022  -0.017   0.385  1.00  0.00      A    N  
+ATOM    211  CA  ARG A  13      -3.626   1.186   1.026  1.00  0.00      A    C  
+ATOM    212  C   ARG A  13      -3.046   1.594   2.333  1.00  0.00      A    C  
+ATOM    213  O   ARG A  13      -2.802   2.758   2.510  1.00  0.00      A    O  
+ATOM    214  CB  ARG A  13      -5.248   1.116   1.109  1.00  0.00      A    C  
+ATOM    215  CG  ARG A  13      -5.956   1.597  -0.197  1.00  0.00      A    C  
+ATOM    216  CD  ARG A  13      -5.906   3.059  -0.606  1.00  0.00      A    C  
+ATOM    217  NE  ARG A  13      -6.717   4.025   0.100  1.00  0.00      A    N  
+ATOM    218  CZ  ARG A  13      -7.018   5.245  -0.194  1.00  0.00      A    C  
+ATOM    219  NH1 ARG A  13      -6.419   5.789  -1.155  1.00  0.00      A    N  
+ATOM    220  NH2 ARG A  13      -7.969   5.915   0.391  1.00  0.00      A    N  
+ATOM    221  H   ARG A  13      -3.651  -0.806   0.412  1.00  0.00      A    H  
+ATOM    222  HA  ARG A  13      -3.354   2.055   0.426  1.00  0.00      A    H  
+ATOM    223  HB2 ARG A  13      -5.577   0.083   1.223  1.00  0.00      A    H  
+ATOM    224  HB3 ARG A  13      -5.569   1.716   1.961  1.00  0.00      A    H  
+ATOM    225  HG2 ARG A  13      -5.472   1.144  -1.062  1.00  0.00      A    H  
+ATOM    226  HG3 ARG A  13      -6.978   1.235  -0.308  1.00  0.00      A    H  
+ATOM    227  HD2 ARG A  13      -4.870   3.386  -0.517  1.00  0.00      A    H  
+ATOM    228  HD3 ARG A  13      -6.189   3.223  -1.646  1.00  0.00      A    H  
+ATOM    229  HE  ARG A  13      -7.264   3.704   0.886  1.00  0.00      A    H  
+ATOM    230 HH11 ARG A  13      -5.643   5.289  -1.564  1.00  0.00      A    H  
+ATOM    231 HH12 ARG A  13      -6.777   6.648  -1.547  1.00  0.00      A    H  
+ATOM    232 HH21 ARG A  13      -8.701   5.374   0.830  1.00  0.00      A    H  
+ATOM    233 HH22 ARG A  13      -8.095   6.917   0.359  1.00  0.00      A    H  
+ATOM    234  N   ASN A  14      -2.854   0.636   3.236  1.00  0.00      A    N  
+ATOM    235  CA  ASN A  14      -2.067   0.849   4.448  1.00  0.00      A    C  
+ATOM    236  C   ASN A  14      -0.584   1.100   4.137  1.00  0.00      A    C  
+ATOM    237  O   ASN A  14      -0.055   2.097   4.616  1.00  0.00      A    O  
+ATOM    238  CB  ASN A  14      -2.234  -0.422   5.351  1.00  0.00      A    C  
+ATOM    239  CG  ASN A  14      -3.603  -0.696   6.023  1.00  0.00      A    C  
+ATOM    240  OD1 ASN A  14      -4.709  -0.597   5.493  1.00  0.00      A    O  
+ATOM    241  ND2 ASN A  14      -3.497  -0.990   7.271  1.00  0.00      A    N  
+ATOM    242  H   ASN A  14      -3.070  -0.350   3.203  1.00  0.00      A    H  
+ATOM    243  HA  ASN A  14      -2.480   1.711   4.971  1.00  0.00      A    H  
+ATOM    244  HB2 ASN A  14      -2.017  -1.329   4.787  1.00  0.00      A    H  
+ATOM    245  HB3 ASN A  14      -1.557  -0.344   6.201  1.00  0.00      A    H  
+ATOM    246 HD21 ASN A  14      -2.626  -1.051   7.779  1.00  0.00      A    H  
+ATOM    247 HD22 ASN A  14      -4.398  -0.992   7.727  1.00  0.00      A    H  
+ATOM    248  N   GLU A  15       0.038   0.373   3.181  1.00  0.00      A    N  
+ATOM    249  CA  GLU A  15       1.447   0.664   2.798  1.00  0.00      A    C  
+ATOM    250  C   GLU A  15       1.854   1.983   2.068  1.00  0.00      A    C  
+ATOM    251  O   GLU A  15       1.088   2.804   1.654  1.00  0.00      A    O  
+ATOM    252  CB  GLU A  15       2.024  -0.623   2.031  1.00  0.00      A    C  
+ATOM    253  CG  GLU A  15       2.858  -1.513   3.017  1.00  0.00      A    C  
+ATOM    254  CD  GLU A  15       4.290  -0.986   3.243  1.00  0.00      A    C  
+ATOM    255  OE1 GLU A  15       5.244  -1.785   3.311  1.00  0.00      A    O  
+ATOM    256  OE2 GLU A  15       4.543   0.288   3.264  1.00  0.00      A    O  
+ATOM    257  H   GLU A  15      -0.385  -0.438   2.752  1.00  0.00      A    H  
+ATOM    258  HA  GLU A  15       1.960   0.610   3.758  1.00  0.00      A    H  
+ATOM    259  HB2 GLU A  15       1.107  -1.131   1.734  1.00  0.00      A    H  
+ATOM    260  HB3 GLU A  15       2.635  -0.419   1.152  1.00  0.00      A    H  
+ATOM    261  HG2 GLU A  15       2.499  -1.367   4.036  1.00  0.00      A    H  
+ATOM    262  HG3 GLU A  15       2.960  -2.487   2.538  1.00  0.00      A    H  
+ATOM    263  N   LYS A  16       3.143   2.204   1.720  1.00  0.00      A    N  
+ATOM    264  CA  LYS A  16       3.742   3.170   0.730  1.00  0.00      A    C  
+ATOM    265  C   LYS A  16       4.387   2.656  -0.543  1.00  0.00      A    C  
+ATOM    266  O   LYS A  16       5.100   3.436  -1.140  1.00  0.00      A    O  
+ATOM    267  CB  LYS A  16       4.712   4.153   1.473  1.00  0.00      A    C  
+ATOM    268  CG  LYS A  16       6.029   3.726   2.021  1.00  0.00      A    C  
+ATOM    269  CD  LYS A  16       6.768   4.863   2.651  1.00  0.00      A    C  
+ATOM    270  CE  LYS A  16       6.546   4.584   4.140  1.00  0.00      A    C  
+ATOM    271  NZ  LYS A  16       6.922   5.681   5.047  1.00  0.00      A    N  
+ATOM    272  H   LYS A  16       3.823   1.635   2.203  1.00  0.00      A    H  
+ATOM    273  HA  LYS A  16       2.907   3.763   0.358  1.00  0.00      A    H  
+ATOM    274  HB2 LYS A  16       4.879   4.985   0.789  1.00  0.00      A    H  
+ATOM    275  HB3 LYS A  16       4.170   4.555   2.329  1.00  0.00      A    H  
+ATOM    276  HG2 LYS A  16       5.874   2.861   2.666  1.00  0.00      A    H  
+ATOM    277  HG3 LYS A  16       6.567   3.533   1.093  1.00  0.00      A    H  
+ATOM    278  HD2 LYS A  16       7.850   4.829   2.527  1.00  0.00      A    H  
+ATOM    279  HD3 LYS A  16       6.416   5.865   2.404  1.00  0.00      A    H  
+ATOM    280  HE2 LYS A  16       5.489   4.408   4.339  1.00  0.00      A    H  
+ATOM    281  HE3 LYS A  16       7.192   3.727   4.330  1.00  0.00      A    H  
+ATOM    282  HZ1 LYS A  16       6.763   5.317   5.975  1.00  0.00      A    H  
+ATOM    283  HZ2 LYS A  16       6.350   6.513   5.069  1.00  0.00      A    H  
+ATOM    284  HZ3 LYS A  16       7.908   5.898   5.003  1.00  0.00      A    H  
+ATOM    285  N   GLU A  17       4.094   1.423  -1.000  1.00  0.00      A    N  
+ATOM    286  CA  GLU A  17       4.451   0.987  -2.365  1.00  0.00      A    C  
+ATOM    287  C   GLU A  17       3.339   1.101  -3.443  1.00  0.00      A    C  
+ATOM    288  O   GLU A  17       2.206   1.347  -3.037  1.00  0.00      A    O  
+ATOM    289  CB  GLU A  17       4.750  -0.466  -2.254  1.00  0.00      A    C  
+ATOM    290  CG  GLU A  17       6.023  -1.131  -1.630  1.00  0.00      A    C  
+ATOM    291  CD  GLU A  17       5.976  -2.592  -1.629  1.00  0.00      A    C  
+ATOM    292  OE1 GLU A  17       5.491  -3.163  -2.602  1.00  0.00      A    O  
+ATOM    293  OE2 GLU A  17       6.600  -3.213  -0.745  1.00  0.00      A    O  
+ATOM    294  H   GLU A  17       3.259   1.003  -0.617  1.00  0.00      A    H  
+ATOM    295  HA  GLU A  17       5.334   1.551  -2.666  1.00  0.00      A    H  
+ATOM    296  HB2 GLU A  17       3.900  -0.913  -1.739  1.00  0.00      A    H  
+ATOM    297  HB3 GLU A  17       4.803  -0.658  -3.326  1.00  0.00      A    H  
+ATOM    298  HG2 GLU A  17       6.928  -0.687  -2.047  1.00  0.00      A    H  
+ATOM    299  HG3 GLU A  17       5.984  -0.872  -0.572  1.00  0.00      A    H  
+ATOM    300  N   LEU A  18       3.784   1.097  -4.705  1.00  0.00      A    N  
+ATOM    301  CA  LEU A  18       2.999   1.271  -5.912  1.00  0.00      A    C  
+ATOM    302  C   LEU A  18       2.193   2.600  -5.923  1.00  0.00      A    C  
+ATOM    303  O   LEU A  18       1.076   2.683  -6.452  1.00  0.00      A    O  
+ATOM    304  CB  LEU A  18       2.185   0.063  -6.209  1.00  0.00      A    C  
+ATOM    305  CG  LEU A  18       2.902  -1.281  -6.449  1.00  0.00      A    C  
+ATOM    306  CD1 LEU A  18       1.934  -2.428  -6.377  1.00  0.00      A    C  
+ATOM    307  CD2 LEU A  18       3.745  -1.318  -7.716  1.00  0.00      A    C  
+ATOM    308  H   LEU A  18       4.774   0.977  -4.862  1.00  0.00      A    H  
+ATOM    309  HA  LEU A  18       3.717   1.300  -6.731  1.00  0.00      A    H  
+ATOM    310  HB2 LEU A  18       1.553  -0.048  -5.328  1.00  0.00      A    H  
+ATOM    311  HB3 LEU A  18       1.642   0.169  -7.148  1.00  0.00      A    H  
+ATOM    312  HG  LEU A  18       3.568  -1.407  -5.596  1.00  0.00      A    H  
+ATOM    313 HD11 LEU A  18       0.954  -2.181  -6.786  1.00  0.00      A    H  
+ATOM    314 HD12 LEU A  18       1.764  -2.649  -5.323  1.00  0.00      A    H  
+ATOM    315 HD13 LEU A  18       2.385  -3.262  -6.916  1.00  0.00      A    H  
+ATOM    316 HD21 LEU A  18       3.111  -1.530  -8.577  1.00  0.00      A    H  
+ATOM    317 HD22 LEU A  18       4.399  -2.185  -7.620  1.00  0.00      A    H  
+ATOM    318 HD23 LEU A  18       4.373  -0.442  -7.878  1.00  0.00      A    H  
+ATOM    319  N   ARG A  19       2.758   3.636  -5.453  1.00  0.00      A    N  
+ATOM    320  CA  ARG A  19       2.072   4.980  -5.431  1.00  0.00      A    C  
+ATOM    321  C   ARG A  19       1.827   5.576  -6.758  1.00  0.00      A    C  
+ATOM    322  O   ARG A  19       0.780   6.172  -6.838  1.00  0.00      A    O  
+ATOM    323  CB  ARG A  19       2.820   5.948  -4.435  1.00  0.00      A    C  
+ATOM    324  CG  ARG A  19       2.904   5.520  -2.909  1.00  0.00      A    C  
+ATOM    325  CD  ARG A  19       4.035   6.245  -2.085  1.00  0.00      A    C  
+ATOM    326  NE  ARG A  19       3.789   7.692  -1.994  1.00  0.00      A    N  
+ATOM    327  CZ  ARG A  19       4.479   8.677  -2.565  1.00  0.00      A    C  
+ATOM    328  NH1 ARG A  19       5.247   8.599  -3.627  1.00  0.00      A    N  
+ATOM    329  NH2 ARG A  19       4.338   9.872  -2.036  1.00  0.00      A    N  
+ATOM    330  H   ARG A  19       3.653   3.582  -4.989  1.00  0.00      A    H  
+ATOM    331  HA  ARG A  19       1.104   4.663  -5.042  1.00  0.00      A    H  
+ATOM    332  HB2 ARG A  19       3.856   5.946  -4.772  1.00  0.00      A    H  
+ATOM    333  HB3 ARG A  19       2.420   6.962  -4.453  1.00  0.00      A    H  
+ATOM    334  HG2 ARG A  19       2.050   5.956  -2.390  1.00  0.00      A    H  
+ATOM    335  HG3 ARG A  19       3.102   4.450  -2.837  1.00  0.00      A    H  
+ATOM    336  HD2 ARG A  19       3.842   5.887  -1.073  1.00  0.00      A    H  
+ATOM    337  HD3 ARG A  19       5.031   5.952  -2.417  1.00  0.00      A    H  
+ATOM    338  HE  ARG A  19       3.299   7.932  -1.144  1.00  0.00      A    H  
+ATOM    339 HH11 ARG A  19       5.240   7.682  -4.051  1.00  0.00      A    H  
+ATOM    340 HH12 ARG A  19       5.721   9.409  -4.000  1.00  0.00      A    H  
+ATOM    341 HH21 ARG A  19       3.787  10.126  -1.228  1.00  0.00      A    H  
+ATOM    342 HH22 ARG A  19       4.480  10.708  -2.585  1.00  0.00      A    H  
+ATOM    343  N   ASP A  20       2.606   5.324  -7.794  1.00  0.00      A    N  
+ATOM    344  CA  ASP A  20       2.384   5.861  -9.114  1.00  0.00      A    C  
+ATOM    345  C   ASP A  20       1.125   5.291  -9.751  1.00  0.00      A    C  
+ATOM    346  O   ASP A  20       0.268   6.007 -10.295  1.00  0.00      A    O  
+ATOM    347  CB  ASP A  20       3.591   5.667 -10.091  1.00  0.00      A    C  
+ATOM    348  CG  ASP A  20       4.825   6.395  -9.690  1.00  0.00      A    C  
+ATOM    349  OD1 ASP A  20       4.809   7.101  -8.690  1.00  0.00      A    O  
+ATOM    350  OD2 ASP A  20       5.819   6.420 -10.497  1.00  0.00      A    O  
+ATOM    351  H   ASP A  20       3.348   4.661  -7.616  1.00  0.00      A    H  
+ATOM    352  HA  ASP A  20       2.293   6.945  -9.054  1.00  0.00      A    H  
+ATOM    353  HB2 ASP A  20       3.840   4.625 -10.295  1.00  0.00      A    H  
+ATOM    354  HB3 ASP A  20       3.264   6.030 -11.065  1.00  0.00      A    H  
+ATOM    355  N   PHE A  21       1.049   3.975  -9.692  1.00  0.00      A    N  
+ATOM    356  CA  PHE A  21      -0.102   3.227 -10.218  1.00  0.00      A    C  
+ATOM    357  C   PHE A  21      -1.348   3.453  -9.483  1.00  0.00      A    C  
+ATOM    358  O   PHE A  21      -2.313   3.668 -10.192  1.00  0.00      A    O  
+ATOM    359  CB  PHE A  21       0.096   1.756 -10.271  1.00  0.00      A    C  
+ATOM    360  CG  PHE A  21       1.324   1.319 -10.907  1.00  0.00      A    C  
+ATOM    361  CD1 PHE A  21       1.410   0.973 -12.275  1.00  0.00      A    C  
+ATOM    362  CD2 PHE A  21       2.493   1.224 -10.141  1.00  0.00      A    C  
+ATOM    363  CE1 PHE A  21       2.629   0.658 -12.938  1.00  0.00      A    C  
+ATOM    364  CE2 PHE A  21       3.731   0.975 -10.771  1.00  0.00      A    C  
+ATOM    365  CZ  PHE A  21       3.774   0.619 -12.103  1.00  0.00      A    C  
+ATOM    366  H   PHE A  21       1.867   3.433  -9.456  1.00  0.00      A    H  
+ATOM    367  HA  PHE A  21      -0.261   3.578 -11.237  1.00  0.00      A    H  
+ATOM    368  HB2 PHE A  21       0.062   1.349  -9.260  1.00  0.00      A    H  
+ATOM    369  HB3 PHE A  21      -0.797   1.323 -10.722  1.00  0.00      A    H  
+ATOM    370  HD1 PHE A  21       0.460   0.997 -12.790  1.00  0.00      A    H  
+ATOM    371  HD2 PHE A  21       2.509   1.467  -9.089  1.00  0.00      A    H  
+ATOM    372  HE1 PHE A  21       2.640   0.594 -14.016  1.00  0.00      A    H  
+ATOM    373  HE2 PHE A  21       4.586   0.817 -10.130  1.00  0.00      A    H  
+ATOM    374  HZ  PHE A  21       4.721   0.381 -12.563  1.00  0.00      A    H  
+ATOM    375  N   ILE A  22      -1.395   3.430  -8.157  1.00  0.00      A    N  
+ATOM    376  CA  ILE A  22      -2.673   3.694  -7.468  1.00  0.00      A    C  
+ATOM    377  C   ILE A  22      -3.294   5.077  -7.804  1.00  0.00      A    C  
+ATOM    378  O   ILE A  22      -4.469   5.256  -8.090  1.00  0.00      A    O  
+ATOM    379  CB  ILE A  22      -2.580   3.465  -5.872  1.00  0.00      A    C  
+ATOM    380  CG1 ILE A  22      -2.389   1.999  -5.679  1.00  0.00      A    C  
+ATOM    381  CG2 ILE A  22      -3.679   3.963  -4.928  1.00  0.00      A    C  
+ATOM    382  CD1 ILE A  22      -1.813   1.522  -4.336  1.00  0.00      A    C  
+ATOM    383  H   ILE A  22      -0.583   3.148  -7.627  1.00  0.00      A    H  
+ATOM    384  HA  ILE A  22      -3.323   2.858  -7.724  1.00  0.00      A    H  
+ATOM    385  HB  ILE A  22      -1.641   3.937  -5.583  1.00  0.00      A    H  
+ATOM    386 HG12 ILE A  22      -3.303   1.431  -5.854  1.00  0.00      A    H  
+ATOM    387 HG13 ILE A  22      -1.644   1.648  -6.393  1.00  0.00      A    H  
+ATOM    388 HG21 ILE A  22      -3.386   3.774  -3.895  1.00  0.00      A    H  
+ATOM    389 HG22 ILE A  22      -4.586   3.420  -5.193  1.00  0.00      A    H  
+ATOM    390 HG23 ILE A  22      -3.805   5.042  -5.015  1.00  0.00      A    H  
+ATOM    391 HD11 ILE A  22      -2.353   1.916  -3.475  1.00  0.00      A    H  
+ATOM    392 HD12 ILE A  22      -0.774   1.745  -4.092  1.00  0.00      A    H  
+ATOM    393 HD13 ILE A  22      -1.877   0.435  -4.288  1.00  0.00      A    H  
+ATOM    394  N   GLU A  23      -2.431   6.103  -7.781  1.00  0.00      A    N  
+ATOM    395  CA  GLU A  23      -2.759   7.466  -8.006  1.00  0.00      A    C  
+ATOM    396  C   GLU A  23      -3.209   7.813  -9.404  1.00  0.00      A    C  
+ATOM    397  O   GLU A  23      -3.256   8.965  -9.767  1.00  0.00      A    O  
+ATOM    398  CB  GLU A  23      -1.582   8.400  -7.487  1.00  0.00      A    C  
+ATOM    399  CG  GLU A  23      -1.419   8.361  -5.929  1.00  0.00      A    C  
+ATOM    400  CD  GLU A  23      -2.564   9.086  -5.167  1.00  0.00      A    C  
+ATOM    401  OE1 GLU A  23      -2.706   8.894  -3.960  1.00  0.00      A    O  
+ATOM    402  OE2 GLU A  23      -3.293   9.878  -5.773  1.00  0.00      A    O  
+ATOM    403  H   GLU A  23      -1.488   5.825  -7.549  1.00  0.00      A    H  
+ATOM    404  HA  GLU A  23      -3.614   7.810  -7.423  1.00  0.00      A    H  
+ATOM    405  HB2 GLU A  23      -0.634   8.208  -7.990  1.00  0.00      A    H  
+ATOM    406  HB3 GLU A  23      -1.800   9.418  -7.810  1.00  0.00      A    H  
+ATOM    407  HG2 GLU A  23      -1.363   7.319  -5.612  1.00  0.00      A    H  
+ATOM    408  HG3 GLU A  23      -0.457   8.790  -5.649  1.00  0.00      A    H  
+ATOM    409  N   LYS A  24      -3.269   6.761 -10.225  1.00  0.00      A    N  
+ATOM    410  CA  LYS A  24      -3.589   6.810 -11.637  1.00  0.00      A    C  
+ATOM    411  C   LYS A  24      -2.768   7.800 -12.528  1.00  0.00      A    C  
+ATOM    412  O   LYS A  24      -3.199   8.476 -13.516  1.00  0.00      A    O  
+ATOM    413  CB  LYS A  24      -5.126   6.888 -11.900  1.00  0.00      A    C  
+ATOM    414  CG  LYS A  24      -5.380   6.277 -13.323  1.00  0.00      A    C  
+ATOM    415  CD  LYS A  24      -6.773   6.848 -13.707  1.00  0.00      A    C  
+ATOM    416  CE  LYS A  24      -7.413   6.384 -15.036  1.00  0.00      A    C  
+ATOM    417  NZ  LYS A  24      -7.853   4.924 -14.863  1.00  0.00      A    N  
+ATOM    418  H   LYS A  24      -3.126   5.851  -9.811  1.00  0.00      A    H  
+ATOM    419  HA  LYS A  24      -3.421   5.789 -11.979  1.00  0.00      A    H  
+ATOM    420  HB2 LYS A  24      -5.542   6.226 -11.140  1.00  0.00      A    H  
+ATOM    421  HB3 LYS A  24      -5.622   7.857 -11.854  1.00  0.00      A    H  
+ATOM    422  HG2 LYS A  24      -4.712   6.681 -14.083  1.00  0.00      A    H  
+ATOM    423  HG3 LYS A  24      -5.440   5.189 -13.344  1.00  0.00      A    H  
+ATOM    424  HD2 LYS A  24      -7.522   6.502 -12.995  1.00  0.00      A    H  
+ATOM    425  HD3 LYS A  24      -6.659   7.923 -13.850  1.00  0.00      A    H  
+ATOM    426  HE2 LYS A  24      -8.291   6.991 -15.253  1.00  0.00      A    H  
+ATOM    427  HE3 LYS A  24      -6.776   6.445 -15.919  1.00  0.00      A    H  
+ATOM    428  HZ1 LYS A  24      -8.492   4.798 -14.091  1.00  0.00      A    H  
+ATOM    429  HZ2 LYS A  24      -7.095   4.257 -14.887  1.00  0.00      A    H  
+ATOM    430  HZ3 LYS A  24      -8.414   4.683 -15.667  1.00  0.00      A    H  
+ATOM    431  N   PHE A  25      -1.498   7.886 -12.167  1.00  0.00      A    N  
+ATOM    432  CA  PHE A  25      -0.453   8.639 -12.825  1.00  0.00      A    C  
+ATOM    433  C   PHE A  25       0.387   7.828 -13.793  1.00  0.00      A    C  
+ATOM    434  O   PHE A  25       0.775   6.700 -13.522  1.00  0.00      A    O  
+ATOM    435  CB  PHE A  25       0.452   9.173 -11.726  1.00  0.00      A    C  
+ATOM    436  CG  PHE A  25       1.736   9.761 -12.303  1.00  0.00      A    C  
+ATOM    437  CD1 PHE A  25       2.907   9.005 -12.538  1.00  0.00      A    C  
+ATOM    438  CD2 PHE A  25       1.758  11.178 -12.564  1.00  0.00      A    C  
+ATOM    439  CE1 PHE A  25       4.105   9.587 -13.043  1.00  0.00      A    C  
+ATOM    440  CE2 PHE A  25       2.994  11.728 -13.084  1.00  0.00      A    C  
+ATOM    441  CZ  PHE A  25       4.085  10.962 -13.279  1.00  0.00      A    C  
+ATOM    442  H   PHE A  25      -1.231   7.421 -11.311  1.00  0.00      A    H  
+ATOM    443  HA  PHE A  25      -0.893   9.530 -13.275  1.00  0.00      A    H  
+ATOM    444  HB2 PHE A  25      -0.002  10.009 -11.193  1.00  0.00      A    H  
+ATOM    445  HB3 PHE A  25       0.748   8.413 -11.002  1.00  0.00      A    H  
+ATOM    446  HD1 PHE A  25       2.979   7.945 -12.345  1.00  0.00      A    H  
+ATOM    447  HD2 PHE A  25       0.921  11.788 -12.258  1.00  0.00      A    H  
+ATOM    448  HE1 PHE A  25       4.994   8.998 -13.217  1.00  0.00      A    H  
+ATOM    449  HE2 PHE A  25       2.881  12.757 -13.392  1.00  0.00      A    H  
+ATOM    450  HZ  PHE A  25       4.965  11.501 -13.596  1.00  0.00      A    H  
+ATOM    451  N   LYS A  26       0.696   8.387 -15.072  1.00  0.00      A    N  
+ATOM    452  CA  LYS A  26       1.513   7.610 -16.075  1.00  0.00      A    C  
+ATOM    453  C   LYS A  26       2.702   8.334 -16.546  1.00  0.00      A    C  
+ATOM    454  O   LYS A  26       3.520   7.917 -17.351  1.00  0.00      A    O  
+ATOM    455  CB  LYS A  26       0.566   7.240 -17.203  1.00  0.00      A    C  
+ATOM    456  CG  LYS A  26      -0.557   6.295 -16.712  1.00  0.00      A    C  
+ATOM    457  CD  LYS A  26      -1.581   6.037 -17.844  1.00  0.00      A    C  
+ATOM    458  CE  LYS A  26      -2.532   7.199 -18.062  1.00  0.00      A    C  
+ATOM    459  NZ  LYS A  26      -3.664   6.645 -18.781  1.00  0.00      A    N  
+ATOM    460  H   LYS A  26       0.297   9.279 -15.326  1.00  0.00      A    H  
+ATOM    461  HA  LYS A  26       1.909   6.715 -15.596  1.00  0.00      A    H  
+ATOM    462  HB2 LYS A  26       0.244   8.128 -17.747  1.00  0.00      A    H  
+ATOM    463  HB3 LYS A  26       1.162   6.746 -17.971  1.00  0.00      A    H  
+ATOM    464  HG2 LYS A  26      -0.126   5.320 -16.482  1.00  0.00      A    H  
+ATOM    465  HG3 LYS A  26      -1.081   6.683 -15.839  1.00  0.00      A    H  
+ATOM    466  HD2 LYS A  26      -0.950   5.857 -18.714  1.00  0.00      A    H  
+ATOM    467  HD3 LYS A  26      -2.032   5.073 -17.610  1.00  0.00      A    H  
+ATOM    468  HE2 LYS A  26      -2.799   7.553 -17.066  1.00  0.00      A    H  
+ATOM    469  HE3 LYS A  26      -2.053   8.032 -18.575  1.00  0.00      A    H  
+ATOM    470  HZ1 LYS A  26      -3.320   5.937 -19.414  1.00  0.00      A    H  
+ATOM    471  HZ2 LYS A  26      -4.088   7.285 -19.437  1.00  0.00      A    H  
+ATOM    472  HZ3 LYS A  26      -4.371   6.208 -18.207  1.00  0.00      A    H  
+ATOM    473  N   GLY A  27       2.925   9.560 -16.181  1.00  0.00      A    N  
+ATOM    474  CA  GLY A  27       3.925  10.536 -16.724  1.00  0.00      A    C  
+ATOM    475  C   GLY A  27       3.505  11.237 -18.002  1.00  0.00      A    C  
+ATOM    476  O   GLY A  27       2.515  10.891 -18.640  1.00  0.00      A    O  
+ATOM    477  H   GLY A  27       2.449   9.820 -15.329  1.00  0.00      A    H  
+ATOM    478  HA2 GLY A  27       3.974  11.288 -15.937  1.00  0.00      A    H  
+ATOM    479  HA3 GLY A  27       4.845   9.957 -16.805  1.00  0.00      A    H  
+ATOM    480  N   ARG A  28       4.361  12.092 -18.555  1.00  0.00      A    N  
+ATOM    481  CA  ARG A  28       4.198  12.643 -19.927  1.00  0.00      A    C  
+ATOM    482  C   ARG A  28       4.508  11.676 -21.108  1.00  0.00      A    C  
+ATOM    483  O   ARG A  28       5.715  11.485 -21.411  1.00  0.00      A    O  
+ATOM    484  CB  ARG A  28       4.721  14.125 -20.019  1.00  0.00      A    C  
+ATOM    485  CG  ARG A  28       6.244  14.390 -19.960  1.00  0.00      A    C  
+ATOM    486  CD  ARG A  28       6.638  15.892 -19.830  1.00  0.00      A    C  
+ATOM    487  NE  ARG A  28       6.120  16.567 -18.672  1.00  0.00      A    N  
+ATOM    488  CZ  ARG A  28       6.549  16.544 -17.395  1.00  0.00      A    C  
+ATOM    489  NH1 ARG A  28       7.641  15.897 -17.049  1.00  0.00      A    N  
+ATOM    490  NH2 ARG A  28       5.992  17.092 -16.384  1.00  0.00      A    N  
+ATOM    491  OXT ARG A  28       3.581  10.995 -21.640  1.00  0.00      A    O  
+ATOM    492  H   ARG A  28       5.119  12.430 -17.980  1.00  0.00      A    H  
+ATOM    493  HA  ARG A  28       3.136  12.803 -20.116  1.00  0.00      A    H  
+ATOM    494  HB2 ARG A  28       4.447  14.543 -20.988  1.00  0.00      A    H  
+ATOM    495  HB3 ARG A  28       4.368  14.713 -19.172  1.00  0.00      A    H  
+ATOM    496  HG2 ARG A  28       6.640  13.731 -19.187  1.00  0.00      A    H  
+ATOM    497  HG3 ARG A  28       6.596  13.953 -20.894  1.00  0.00      A    H  
+ATOM    498  HD2 ARG A  28       7.719  15.846 -19.699  1.00  0.00      A    H  
+ATOM    499  HD3 ARG A  28       6.516  16.420 -20.776  1.00  0.00      A    H  
+ATOM    500  HE  ARG A  28       5.316  17.165 -18.795  1.00  0.00      A    H  
+ATOM    501 HH11 ARG A  28       8.207  15.416 -17.733  1.00  0.00      A    H  
+ATOM    502 HH12 ARG A  28       7.972  15.597 -16.143  1.00  0.00      A    H  
+ATOM    503 HH21 ARG A  28       5.062  17.442 -16.564  1.00  0.00      A    H  
+ATOM    504 HH22 ARG A  28       6.402  16.979 -15.468  1.00  0.00      A    H  
+ENDMDL
+END

entangled-tps/data/bbl/bbl.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5f1bc7e9cc2cfea8490cae88ee65bc1e2695c9ecbb15b6c25e1a029dbafd54f5
+size 28951641

entangled-tps/data/bbl/folded.pdb

@@ -0,0 +1,917 @@
+HEADER    TRANSFERASE                             06-NOV-09   2WXC              
+TITLE     THE FOLDING MECHANISM OF BBL: PLASTICITY OF TRANSITION-STATE STRUCTURE
+TITLE    2 OBSERVED WITHIN AN ULTRAFAST FOLDING PROTEIN FAMILY.                 
+COMPND    MOL_ID: 1;                                                            
+COMPND   2 MOLECULE: DIHYDROLIPOYLTRANSSUCCINASE;                               
+COMPND   3 CHAIN: A;                                                            
+COMPND   4 FRAGMENT: RESIDUES 109-153;                                          
+COMPND   5 EC: 2.3.1.61;                                                        
+COMPND   6 ENGINEERED: YES;                                                     
+COMPND   7 MUTATION: YES                                                        
+SOURCE    MOL_ID: 1;                                                            
+SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                               
+SOURCE   3 ORGANISM_TAXID: 562;                                                 
+SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
+SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562;                                        
+SOURCE   6 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA                            
+KEYWDS    LIPOYL, TRANSFERASE, ACYLTRANSFERASE                                  
+EXPDTA    SOLUTION NMR                                                          
+NUMMDL    20                                                                    
+AUTHOR    H.NEUWEILER,T.D.SHARPE,T.J.RUTHERFORD,C.M.JOHNSON,M.D.ALLEN,          
+AUTHOR   2 N.FERGUSON,A.R.FERSHT                                                
+REVDAT   3   15-MAY-24 2WXC    1       REMARK                                   
+REVDAT   2   19-APR-17 2WXC    1       REMARK                                   
+REVDAT   1   17-NOV-09 2WXC    0                                                
+SPRSDE     17-NOV-09 2WXC      2WAV                                             
+JRNL        AUTH   H.NEUWEILER,T.D.SHARPE,T.J.RUTHERFORD,C.M.JOHNSON,M.D.ALLEN, 
+JRNL        AUTH 2 N.FERGUSON,A.R.FERSHT                                        
+JRNL        TITL   THE FOLDING MECHANISM OF BBL: PLASTICITY OF TRANSITION-STATE 
+JRNL        TITL 2 STRUCTURE OBSERVED WITHIN AN ULTRAFAST FOLDING PROTEIN       
+JRNL        TITL 3 FAMILY.                                                      
+JRNL        REF    J.MOL.BIOL.                   V. 390  1060 2009              
+JRNL        REFN                   ISSN 0022-2836                               
+JRNL        PMID   19445954                                                     
+JRNL        DOI    10.1016/J.JMB.2009.05.011                                    
+REMARK   2                                                                      
+REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
+REMARK   3                                                                      
+REMARK   3 REFINEMENT.                                                          
+REMARK   3   PROGRAM     : CNS 1.1                                              
+REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
+REMARK   3                 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,   
+REMARK   3                 SIMONSON,WARREN                                      
+REMARK   3                                                                      
+REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
+REMARK   4                                                                      
+REMARK   4 2WXC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
+REMARK 100                                                                      
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-NOV-09.                  
+REMARK 100 THE DEPOSITION ID IS D_1290041668.                                   
+REMARK 210                                                                      
+REMARK 210 EXPERIMENTAL DETAILS                                                 
+REMARK 210  EXPERIMENT TYPE                : NMR                                
+REMARK 210  TEMPERATURE           (KELVIN) : 298.0                              
+REMARK 210  PH                             : 7.0                                
+REMARK 210  IONIC STRENGTH                 : NULL                               
+REMARK 210  PRESSURE                       : 1.0 ATM                            
+REMARK 210  SAMPLE CONTENTS                : 10% WATER/90% D2O                  
+REMARK 210                                                                      
+REMARK 210  NMR EXPERIMENTS CONDUCTED      : NULL                               
+REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ; 800 MHZ; 500 MHZ          
+REMARK 210  SPECTROMETER MODEL             : AVANCE; DMX                        
+REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
+REMARK 210                                                                      
+REMARK 210  STRUCTURE DETERMINATION.                                            
+REMARK 210   SOFTWARE USED                 : ANSIG 3.3                          
+REMARK 210   METHOD USED                   : CNS                                
+REMARK 210                                                                      
+REMARK 210 CONFORMERS, NUMBER CALCULATED   : 20                                 
+REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
+REMARK 210 CONFORMERS, SELECTION CRITERIA  : NO VIOLATIONS                      
+REMARK 210                                                                      
+REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
+REMARK 210                                                                      
+REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR      
+REMARK 210  SPECTROSCOPY ON 13C, 15N-LABELED MATERIAL AND BU 1H METHODS         
+REMARK 215                                                                      
+REMARK 215 NMR STUDY                                                            
+REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
+REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
+REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
+REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
+REMARK 300                                                                      
+REMARK 300 BIOMOLECULE: 1                                                       
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
+REMARK 300 BURIED SURFACE AREA.                                                 
+REMARK 350                                                                      
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
+REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
+REMARK 350                                                                      
+REMARK 350 BIOMOLECULE: 1                                                       
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 400                                                                      
+REMARK 400 COMPOUND                                                             
+REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 125 TO TRP                        
+REMARK 500                                                                      
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
+REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
+REMARK 500                                                                      
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
+REMARK 500                                                                      
+REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
+REMARK 500                                                                      
+REMARK 500 REMARK: NULL                                                         
+REMARK 500                                                                      
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
+REMARK 500 SUBTOPIC: TORSION ANGLES                                             
+REMARK 500                                                                      
+REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
+REMARK 500                                                                      
+REMARK 500 STANDARD TABLE:                                                      
+REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
+REMARK 500                                                                      
+REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
+REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
+REMARK 500                                                                      
+REMARK 500  M RES CSSEQI        PSI       PHI                                   
+REMARK 500  1 ASN A 127      -56.99   -176.59                                   
+REMARK 500  1 THR A 152       75.34   -166.97                                   
+REMARK 500  1 VAL A 154       38.88   -145.01                                   
+REMARK 500  2 ASN A 128       77.69   -117.27                                   
+REMARK 500  2 ASP A 129       81.93     61.13                                   
+REMARK 500  2 VAL A 154       97.06     59.60                                   
+REMARK 500  2 LYS A 169       42.53   -107.72                                   
+REMARK 500  3 SER A 125      -41.83   -174.18                                   
+REMARK 500  3 VAL A 154      -66.52   -128.07                                   
+REMARK 500  4 SER A 125       78.26     61.16                                   
+REMARK 500  4 ASN A 127      -55.46   -125.66                                   
+REMARK 500  4 LYS A 169       40.04   -104.93                                   
+REMARK 500  6 SER A 125      -41.86   -172.89                                   
+REMARK 500  6 GLN A 126       86.60    -66.89                                   
+REMARK 500  6 VAL A 154      117.49   -176.56                                   
+REMARK 500  7 ASN A 127     -176.99     58.97                                   
+REMARK 500  7 ASP A 129       79.62   -118.99                                   
+REMARK 500  7 THR A 152       35.51   -172.29                                   
+REMARK 500  7 VAL A 154       60.30   -178.20                                   
+REMARK 500  7 ARG A 157      147.59   -177.35                                   
+REMARK 500  8 LYS A 169       61.40   -115.08                                   
+REMARK 500  9 SER A 125      -68.65   -133.05                                   
+REMARK 500  9 GLN A 126       84.50     59.92                                   
+REMARK 500  9 ASN A 127      -46.99   -157.68                                   
+REMARK 500  9 ASN A 128      -74.26    -79.09                                   
+REMARK 500  9 ASP A 129      152.20     61.54                                   
+REMARK 500  9 VAL A 154      -67.66     69.25                                   
+REMARK 500  9 LYS A 169       35.29    -96.97                                   
+REMARK 500 10 ASN A 128       41.95   -150.05                                   
+REMARK 500 10 VAL A 154      -54.39   -135.90                                   
+REMARK 500 10 LYS A 169       68.50   -112.16                                   
+REMARK 500 11 GLN A 126       31.26   -162.46                                   
+REMARK 500 11 ASN A 128      169.74     60.39                                   
+REMARK 500 11 LYS A 169       34.83    -98.40                                   
+REMARK 500 12 ASN A 128       98.11     61.75                                   
+REMARK 500 12 ASP A 129      -56.99   -120.24                                   
+REMARK 500 12 THR A 152       62.97   -114.42                                   
+REMARK 500 12 VAL A 154      -46.08   -147.26                                   
+REMARK 500 12 LYS A 169       48.67    -92.96                                   
+REMARK 500 13 SER A 125      -57.88   -164.71                                   
+REMARK 500 13 VAL A 154       51.81   -174.22                                   
+REMARK 500 14 GLN A 126       99.86     60.44                                   
+REMARK 500 14 THR A 152       32.54   -163.83                                   
+REMARK 500 14 LYS A 169       42.84    -95.63                                   
+REMARK 500 15 ASP A 129       80.39   -163.11                                   
+REMARK 500 15 THR A 152      -70.82   -139.61                                   
+REMARK 500 15 VAL A 154      -44.96   -158.72                                   
+REMARK 500 16 SER A 125       33.57   -163.35                                   
+REMARK 500 16 THR A 152       36.21    -97.85                                   
+REMARK 500 17 ASN A 128       42.03   -104.81                                   
+REMARK 500                                                                      
+REMARK 500 THIS ENTRY HAS      62 RAMACHANDRAN OUTLIERS.                        
+REMARK 500                                                                      
+REMARK 500 REMARK: NULL                                                         
+REMARK 999                                                                      
+REMARK 999 SEQUENCE                                                             
+REMARK 999 HIS-TRP POINT MUTATION WAS INTRODUCED TO ENABLE FOLDING              
+REMARK 999 ANALYSIS                                                             
+DBREF  2WXC A  124   125  PDB    2WXC     2WXC           124    125             
+DBREF  2WXC A  126   170  UNP    B7M5P0   B7M5P0_ECO8A   109    153             
+SEQADV 2WXC TRP A  142  UNP  B7M5P0    HIS   125 ENGINEERED MUTATION            
+SEQRES   1 A   47  GLY SER GLN ASN ASN ASP ALA LEU SER PRO ALA ILE ARG          
+SEQRES   2 A   47  ARG LEU LEU ALA GLU TRP ASN LEU ASP ALA SER ALA ILE          
+SEQRES   3 A   47  LYS GLY THR GLY VAL GLY GLY ARG LEU THR ARG GLU ASP          
+SEQRES   4 A   47  VAL GLU LYS HIS LEU ALA LYS ALA                              
+HELIX    1   1 SER A  132  ASN A  143  1                                  12    
+HELIX    2   2 ASP A  145  ILE A  149  5                                   5    
+HELIX    3   3 THR A  159  ALA A  170  1                                  12    
+CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      1.000000  0.000000  0.000000        0.00000                         
+SCALE2      0.000000  1.000000  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  1.000000        0.00000                         
+MODEL        1                                                                  
+ATOM      1  N   GLY A 124      -7.122 -14.918  15.009  1.00  0.00           N  
+ATOM      2  CA  GLY A 124      -7.128 -13.588  15.678  1.00  0.00           C  
+ATOM      3  C   GLY A 124      -7.129 -12.440  14.689  1.00  0.00           C  
+ATOM      4  O   GLY A 124      -8.187 -11.935  14.313  1.00  0.00           O  
+ATOM      5  H1  GLY A 124      -7.460 -14.826  14.030  1.00  0.00           H  
+ATOM      6  H2  GLY A 124      -6.158 -15.307  14.997  1.00  0.00           H  
+ATOM      7  H3  GLY A 124      -7.743 -15.577  15.518  1.00  0.00           H  
+ATOM      8  HA2 GLY A 124      -8.009 -13.513  16.299  1.00  0.00           H  
+ATOM      9  HA3 GLY A 124      -6.253 -13.508  16.306  1.00  0.00           H  
+ATOM     10  N   SER A 125      -5.938 -12.025  14.266  1.00  0.00           N  
+ATOM     11  CA  SER A 125      -5.805 -10.929  13.313  1.00  0.00           C  
+ATOM     12  C   SER A 125      -5.331 -11.442  11.957  1.00  0.00           C  
+ATOM     13  O   SER A 125      -5.677 -10.884  10.916  1.00  0.00           O  
+ATOM     14  CB  SER A 125      -4.825  -9.881  13.845  1.00  0.00           C  
+ATOM     15  OG  SER A 125      -3.537 -10.438  14.041  1.00  0.00           O  
+ATOM     16  H   SER A 125      -5.131 -12.468  14.602  1.00  0.00           H  
+ATOM     17  HA  SER A 125      -6.776 -10.473  13.193  1.00  0.00           H  
+ATOM     18  HB2 SER A 125      -4.749  -9.071  13.136  1.00  0.00           H  
+ATOM     19  HB3 SER A 125      -5.187  -9.500  14.789  1.00  0.00           H  
+ATOM     20  HG  SER A 125      -3.021  -9.861  14.607  1.00  0.00           H  
+ATOM     21  N   GLN A 126      -4.537 -12.508  11.978  1.00  0.00           N  
+ATOM     22  CA  GLN A 126      -4.015 -13.096  10.749  1.00  0.00           C  
+ATOM     23  C   GLN A 126      -5.111 -13.843   9.996  1.00  0.00           C  
+ATOM     24  O   GLN A 126      -5.719 -14.773  10.526  1.00  0.00           O  
+ATOM     25  CB  GLN A 126      -2.860 -14.047  11.066  1.00  0.00           C  
+ATOM     26  CG  GLN A 126      -1.515 -13.349  11.188  1.00  0.00           C  
+ATOM     27  CD  GLN A 126      -0.376 -14.318  11.436  1.00  0.00           C  
+ATOM     28  OE1 GLN A 126      -0.584 -15.423  11.938  1.00  0.00           O  
+ATOM     29  NE2 GLN A 126       0.838 -13.907  11.086  1.00  0.00           N  
+ATOM     30  H   GLN A 126      -4.296 -12.908  12.839  1.00  0.00           H  
+ATOM     31  HA  GLN A 126      -3.650 -12.294  10.127  1.00  0.00           H  
+ATOM     32  HB2 GLN A 126      -3.067 -14.549  11.999  1.00  0.00           H  
+ATOM     33  HB3 GLN A 126      -2.788 -14.783  10.279  1.00  0.00           H  
+ATOM     34  HG2 GLN A 126      -1.317 -12.813  10.272  1.00  0.00           H  
+ATOM     35  HG3 GLN A 126      -1.560 -12.651  12.011  1.00  0.00           H  
+ATOM     36 HE21 GLN A 126       0.928 -13.014  10.692  1.00  0.00           H  
+ATOM     37 HE22 GLN A 126       1.592 -14.514  11.235  1.00  0.00           H  
+ATOM     38  N   ASN A 127      -5.358 -13.430   8.757  1.00  0.00           N  
+ATOM     39  CA  ASN A 127      -6.381 -14.060   7.931  1.00  0.00           C  
+ATOM     40  C   ASN A 127      -6.401 -13.452   6.532  1.00  0.00           C  
+ATOM     41  O   ASN A 127      -6.247 -14.157   5.535  1.00  0.00           O  
+ATOM     42  CB  ASN A 127      -7.757 -13.914   8.588  1.00  0.00           C  
+ATOM     43  CG  ASN A 127      -8.334 -15.247   9.025  1.00  0.00           C  
+ATOM     44  OD1 ASN A 127      -8.196 -15.645  10.182  1.00  0.00           O  
+ATOM     45  ND2 ASN A 127      -8.981 -15.944   8.099  1.00  0.00           N  
+ATOM     46  H   ASN A 127      -4.840 -12.683   8.390  1.00  0.00           H  
+ATOM     47  HA  ASN A 127      -6.141 -15.109   7.850  1.00  0.00           H  
+ATOM     48  HB2 ASN A 127      -7.669 -13.280   9.457  1.00  0.00           H  
+ATOM     49  HB3 ASN A 127      -8.441 -13.460   7.885  1.00  0.00           H  
+ATOM     50 HD21 ASN A 127      -9.051 -15.564   7.199  1.00  0.00           H  
+ATOM     51 HD22 ASN A 127      -9.364 -16.808   8.355  1.00  0.00           H  
+ATOM     52  N   ASN A 128      -6.590 -12.137   6.466  1.00  0.00           N  
+ATOM     53  CA  ASN A 128      -6.629 -11.434   5.190  1.00  0.00           C  
+ATOM     54  C   ASN A 128      -5.697 -10.227   5.206  1.00  0.00           C  
+ATOM     55  O   ASN A 128      -5.769  -9.387   6.103  1.00  0.00           O  
+ATOM     56  CB  ASN A 128      -8.057 -10.986   4.872  1.00  0.00           C  
+ATOM     57  CG  ASN A 128      -8.604 -10.020   5.905  1.00  0.00           C  
+ATOM     58  OD1 ASN A 128      -9.305 -10.418   6.835  1.00  0.00           O  
+ATOM     59  ND2 ASN A 128      -8.285  -8.741   5.745  1.00  0.00           N  
+ATOM     60  H   ASN A 128      -6.706 -11.630   7.296  1.00  0.00           H  
+ATOM     61  HA  ASN A 128      -6.298 -12.118   4.424  1.00  0.00           H  
+ATOM     62  HB2 ASN A 128      -8.070 -10.499   3.909  1.00  0.00           H  
+ATOM     63  HB3 ASN A 128      -8.700 -11.853   4.841  1.00  0.00           H  
+ATOM     64 HD21 ASN A 128      -7.723  -8.496   4.981  1.00  0.00           H  
+ATOM     65 HD22 ASN A 128      -8.625  -8.094   6.398  1.00  0.00           H  
+ATOM     66  N   ASP A 129      -4.822 -10.147   4.209  1.00  0.00           N  
+ATOM     67  CA  ASP A 129      -3.875  -9.042   4.109  1.00  0.00           C  
+ATOM     68  C   ASP A 129      -4.537  -7.810   3.501  1.00  0.00           C  
+ATOM     69  O   ASP A 129      -5.453  -7.923   2.687  1.00  0.00           O  
+ATOM     70  CB  ASP A 129      -2.666  -9.456   3.266  1.00  0.00           C  
+ATOM     71  CG  ASP A 129      -1.474  -9.847   4.117  1.00  0.00           C  
+ATOM     72  OD1 ASP A 129      -1.257  -9.204   5.166  1.00  0.00           O  
+ATOM     73  OD2 ASP A 129      -0.757 -10.796   3.735  1.00  0.00           O  
+ATOM     74  H   ASP A 129      -4.813 -10.848   3.524  1.00  0.00           H  
+ATOM     75  HA  ASP A 129      -3.540  -8.801   5.107  1.00  0.00           H  
+ATOM     76  HB2 ASP A 129      -2.937 -10.300   2.650  1.00  0.00           H  
+ATOM     77  HB3 ASP A 129      -2.377  -8.630   2.631  1.00  0.00           H  
+ATOM     78  N   ALA A 130      -4.064  -6.634   3.899  1.00  0.00           N  
+ATOM     79  CA  ALA A 130      -4.607  -5.379   3.392  1.00  0.00           C  
+ATOM     80  C   ALA A 130      -3.829  -4.890   2.171  1.00  0.00           C  
+ATOM     81  O   ALA A 130      -3.974  -3.740   1.750  1.00  0.00           O  
+ATOM     82  CB  ALA A 130      -4.594  -4.321   4.484  1.00  0.00           C  
+ATOM     83  H   ALA A 130      -3.331  -6.608   4.550  1.00  0.00           H  
+ATOM     84  HA  ALA A 130      -5.634  -5.554   3.107  1.00  0.00           H  
+ATOM     85  HB1 ALA A 130      -4.573  -4.802   5.451  1.00  0.00           H  
+ATOM     86  HB2 ALA A 130      -5.482  -3.711   4.405  1.00  0.00           H  
+ATOM     87  HB3 ALA A 130      -3.719  -3.698   4.372  1.00  0.00           H  
+ATOM     88  N   LEU A 131      -2.999  -5.765   1.607  1.00  0.00           N  
+ATOM     89  CA  LEU A 131      -2.199  -5.413   0.440  1.00  0.00           C  
+ATOM     90  C   LEU A 131      -2.149  -6.552  -0.569  1.00  0.00           C  
+ATOM     91  O   LEU A 131      -2.534  -7.683  -0.273  1.00  0.00           O  
+ATOM     92  CB  LEU A 131      -0.771  -5.061   0.857  1.00  0.00           C  
+ATOM     93  CG  LEU A 131      -0.628  -3.900   1.839  1.00  0.00           C  
+ATOM     94  CD1 LEU A 131      -1.464  -2.704   1.401  1.00  0.00           C  
+ATOM     95  CD2 LEU A 131      -1.010  -4.341   3.247  1.00  0.00           C  
+ATOM     96  H   LEU A 131      -2.922  -6.667   1.983  1.00  0.00           H  
+ATOM     97  HA  LEU A 131      -2.652  -4.553  -0.027  1.00  0.00           H  
+ATOM     98  HB2 LEU A 131      -0.328  -5.937   1.307  1.00  0.00           H  
+ATOM     99  HB3 LEU A 131      -0.213  -4.818  -0.032  1.00  0.00           H  
+ATOM    100  HG  LEU A 131       0.405  -3.588   1.855  1.00  0.00           H  
+ATOM    101 HD11 LEU A 131      -1.944  -2.923   0.459  1.00  0.00           H  
+ATOM    102 HD12 LEU A 131      -2.214  -2.493   2.148  1.00  0.00           H  
+ATOM    103 HD13 LEU A 131      -0.822  -1.847   1.283  1.00  0.00           H  
+ATOM    104 HD21 LEU A 131      -1.338  -5.371   3.226  1.00  0.00           H  
+ATOM    105 HD22 LEU A 131      -0.152  -4.251   3.896  1.00  0.00           H  
+ATOM    106 HD23 LEU A 131      -1.810  -3.717   3.617  1.00  0.00           H  
+ATOM    107  N   SER A 132      -1.646  -6.239  -1.756  1.00  0.00           N  
+ATOM    108  CA  SER A 132      -1.507  -7.224  -2.817  1.00  0.00           C  
+ATOM    109  C   SER A 132      -0.045  -7.644  -2.943  1.00  0.00           C  
+ATOM    110  O   SER A 132       0.817  -7.121  -2.238  1.00  0.00           O  
+ATOM    111  CB  SER A 132      -2.012  -6.654  -4.145  1.00  0.00           C  
+ATOM    112  OG  SER A 132      -2.846  -7.583  -4.815  1.00  0.00           O  
+ATOM    113  H   SER A 132      -1.342  -5.323  -1.916  1.00  0.00           H  
+ATOM    114  HA  SER A 132      -2.099  -8.087  -2.552  1.00  0.00           H  
+ATOM    115  HB2 SER A 132      -2.577  -5.754  -3.956  1.00  0.00           H  
+ATOM    116  HB3 SER A 132      -1.169  -6.422  -4.780  1.00  0.00           H  
+ATOM    117  HG  SER A 132      -3.547  -7.869  -4.225  1.00  0.00           H  
+ATOM    118  N   PRO A 133       0.259  -8.596  -3.837  1.00  0.00           N  
+ATOM    119  CA  PRO A 133       1.631  -9.074  -4.033  1.00  0.00           C  
+ATOM    120  C   PRO A 133       2.596  -7.954  -4.404  1.00  0.00           C  
+ATOM    121  O   PRO A 133       3.740  -7.934  -3.950  1.00  0.00           O  
+ATOM    122  CB  PRO A 133       1.506 -10.077  -5.185  1.00  0.00           C  
+ATOM    123  CG  PRO A 133       0.072 -10.484  -5.189  1.00  0.00           C  
+ATOM    124  CD  PRO A 133      -0.700  -9.284  -4.718  1.00  0.00           C  
+ATOM    125  HA  PRO A 133       1.998  -9.578  -3.152  1.00  0.00           H  
+ATOM    126  HB2 PRO A 133       1.783  -9.598  -6.113  1.00  0.00           H  
+ATOM    127  HB3 PRO A 133       2.154 -10.922  -5.003  1.00  0.00           H  
+ATOM    128  HG2 PRO A 133      -0.231 -10.755  -6.189  1.00  0.00           H  
+ATOM    129  HG3 PRO A 133      -0.077 -11.313  -4.513  1.00  0.00           H  
+ATOM    130  HD2 PRO A 133      -0.973  -8.658  -5.556  1.00  0.00           H  
+ATOM    131  HD3 PRO A 133      -1.577  -9.589  -4.169  1.00  0.00           H  
+ATOM    132  N   ALA A 134       2.134  -7.023  -5.232  1.00  0.00           N  
+ATOM    133  CA  ALA A 134       2.968  -5.905  -5.659  1.00  0.00           C  
+ATOM    134  C   ALA A 134       3.196  -4.917  -4.523  1.00  0.00           C  
+ATOM    135  O   ALA A 134       4.277  -4.347  -4.395  1.00  0.00           O  
+ATOM    136  CB  ALA A 134       2.349  -5.206  -6.859  1.00  0.00           C  
+ATOM    137  H   ALA A 134       1.215  -7.090  -5.564  1.00  0.00           H  
+ATOM    138  HA  ALA A 134       3.925  -6.307  -5.958  1.00  0.00           H  
+ATOM    139  HB1 ALA A 134       2.095  -5.939  -7.612  1.00  0.00           H  
+ATOM    140  HB2 ALA A 134       3.055  -4.500  -7.270  1.00  0.00           H  
+ATOM    141  HB3 ALA A 134       1.455  -4.684  -6.551  1.00  0.00           H  
+ATOM    142  N   ILE A 135       2.180  -4.721  -3.693  1.00  0.00           N  
+ATOM    143  CA  ILE A 135       2.304  -3.808  -2.567  1.00  0.00           C  
+ATOM    144  C   ILE A 135       3.112  -4.455  -1.457  1.00  0.00           C  
+ATOM    145  O   ILE A 135       3.811  -3.776  -0.716  1.00  0.00           O  
+ATOM    146  CB  ILE A 135       0.937  -3.387  -2.003  1.00  0.00           C  
+ATOM    147  CG1 ILE A 135       0.082  -2.740  -3.095  1.00  0.00           C  
+ATOM    148  CG2 ILE A 135       1.124  -2.433  -0.830  1.00  0.00           C  
+ATOM    149  CD1 ILE A 135      -0.910  -3.688  -3.731  1.00  0.00           C  
+ATOM    150  H   ILE A 135       1.340  -5.205  -3.833  1.00  0.00           H  
+ATOM    151  HA  ILE A 135       2.826  -2.921  -2.908  1.00  0.00           H  
+ATOM    152  HB  ILE A 135       0.439  -4.271  -1.637  1.00  0.00           H  
+ATOM    153 HG12 ILE A 135      -0.473  -1.917  -2.669  1.00  0.00           H  
+ATOM    154 HG13 ILE A 135       0.730  -2.365  -3.874  1.00  0.00           H  
+ATOM    155 HG21 ILE A 135       1.752  -2.900  -0.082  1.00  0.00           H  
+ATOM    156 HG22 ILE A 135       1.592  -1.523  -1.176  1.00  0.00           H  
+ATOM    157 HG23 ILE A 135       0.162  -2.201  -0.398  1.00  0.00           H  
+ATOM    158 HD11 ILE A 135      -0.557  -4.703  -3.625  1.00  0.00           H  
+ATOM    159 HD12 ILE A 135      -1.868  -3.586  -3.244  1.00  0.00           H  
+ATOM    160 HD13 ILE A 135      -1.013  -3.451  -4.780  1.00  0.00           H  
+ATOM    161  N   ARG A 136       3.012  -5.774  -1.345  1.00  0.00           N  
+ATOM    162  CA  ARG A 136       3.751  -6.490  -0.318  1.00  0.00           C  
+ATOM    163  C   ARG A 136       5.245  -6.423  -0.611  1.00  0.00           C  
+ATOM    164  O   ARG A 136       6.058  -6.183   0.286  1.00  0.00           O  
+ATOM    165  CB  ARG A 136       3.293  -7.949  -0.246  1.00  0.00           C  
+ATOM    166  CG  ARG A 136       2.038  -8.154   0.585  1.00  0.00           C  
+ATOM    167  CD  ARG A 136       1.807  -9.626   0.888  1.00  0.00           C  
+ATOM    168  NE  ARG A 136       1.099 -10.304  -0.196  1.00  0.00           N  
+ATOM    169  CZ  ARG A 136      -0.223 -10.283  -0.347  1.00  0.00           C  
+ATOM    170  NH1 ARG A 136      -0.987  -9.614   0.508  1.00  0.00           N  
+ATOM    171  NH2 ARG A 136      -0.785 -10.933  -1.358  1.00  0.00           N  
+ATOM    172  H   ARG A 136       2.434  -6.272  -1.964  1.00  0.00           H  
+ATOM    173  HA  ARG A 136       3.557  -6.006   0.630  1.00  0.00           H  
+ATOM    174  HB2 ARG A 136       3.099  -8.303  -1.247  1.00  0.00           H  
+ATOM    175  HB3 ARG A 136       4.087  -8.541   0.187  1.00  0.00           H  
+ATOM    176  HG2 ARG A 136       2.141  -7.618   1.516  1.00  0.00           H  
+ATOM    177  HG3 ARG A 136       1.190  -7.771   0.038  1.00  0.00           H  
+ATOM    178  HD2 ARG A 136       2.765 -10.104   1.033  1.00  0.00           H  
+ATOM    179  HD3 ARG A 136       1.224  -9.708   1.794  1.00  0.00           H  
+ATOM    180  HE  ARG A 136       1.638 -10.805  -0.844  1.00  0.00           H  
+ATOM    181 HH11 ARG A 136      -0.571  -9.121   1.271  1.00  0.00           H  
+ATOM    182 HH12 ARG A 136      -1.980  -9.603   0.388  1.00  0.00           H  
+ATOM    183 HH21 ARG A 136      -0.215 -11.437  -2.007  1.00  0.00           H  
+ATOM    184 HH22 ARG A 136      -1.778 -10.918  -1.472  1.00  0.00           H  
+ATOM    185  N   ARG A 137       5.606  -6.602  -1.882  1.00  0.00           N  
+ATOM    186  CA  ARG A 137       7.001  -6.530  -2.275  1.00  0.00           C  
+ATOM    187  C   ARG A 137       7.494  -5.102  -2.100  1.00  0.00           C  
+ATOM    188  O   ARG A 137       8.551  -4.862  -1.521  1.00  0.00           O  
+ATOM    189  CB  ARG A 137       7.189  -7.009  -3.723  1.00  0.00           C  
+ATOM    190  CG  ARG A 137       6.996  -5.928  -4.775  1.00  0.00           C  
+ATOM    191  CD  ARG A 137       7.210  -6.470  -6.179  1.00  0.00           C  
+ATOM    192  NE  ARG A 137       8.508  -7.126  -6.321  1.00  0.00           N  
+ATOM    193  CZ  ARG A 137       8.857  -7.856  -7.377  1.00  0.00           C  
+ATOM    194  NH1 ARG A 137       8.011  -8.026  -8.385  1.00  0.00           N  
+ATOM    195  NH2 ARG A 137      10.058  -8.418  -7.426  1.00  0.00           N  
+ATOM    196  H   ARG A 137       4.917  -6.764  -2.566  1.00  0.00           H  
+ATOM    197  HA  ARG A 137       7.563  -7.171  -1.615  1.00  0.00           H  
+ATOM    198  HB2 ARG A 137       8.189  -7.404  -3.829  1.00  0.00           H  
+ATOM    199  HB3 ARG A 137       6.480  -7.800  -3.919  1.00  0.00           H  
+ATOM    200  HG2 ARG A 137       5.992  -5.543  -4.700  1.00  0.00           H  
+ATOM    201  HG3 ARG A 137       7.703  -5.131  -4.595  1.00  0.00           H  
+ATOM    202  HD2 ARG A 137       6.430  -7.185  -6.397  1.00  0.00           H  
+ATOM    203  HD3 ARG A 137       7.153  -5.652  -6.880  1.00  0.00           H  
+ATOM    204  HE  ARG A 137       9.152  -7.018  -5.589  1.00  0.00           H  
+ATOM    205 HH11 ARG A 137       7.104  -7.605  -8.354  1.00  0.00           H  
+ATOM    206 HH12 ARG A 137       8.280  -8.575  -9.176  1.00  0.00           H  
+ATOM    207 HH21 ARG A 137      10.700  -8.293  -6.670  1.00  0.00           H  
+ATOM    208 HH22 ARG A 137      10.321  -8.966  -8.220  1.00  0.00           H  
+ATOM    209  N   LEU A 138       6.694  -4.158  -2.579  1.00  0.00           N  
+ATOM    210  CA  LEU A 138       7.018  -2.744  -2.458  1.00  0.00           C  
+ATOM    211  C   LEU A 138       7.164  -2.365  -0.993  1.00  0.00           C  
+ATOM    212  O   LEU A 138       8.086  -1.653  -0.611  1.00  0.00           O  
+ATOM    213  CB  LEU A 138       5.922  -1.892  -3.106  1.00  0.00           C  
+ATOM    214  CG  LEU A 138       6.206  -1.453  -4.544  1.00  0.00           C  
+ATOM    215  CD1 LEU A 138       5.021  -1.765  -5.444  1.00  0.00           C  
+ATOM    216  CD2 LEU A 138       6.538   0.031  -4.595  1.00  0.00           C  
+ATOM    217  H   LEU A 138       5.853  -4.420  -3.008  1.00  0.00           H  
+ATOM    218  HA  LEU A 138       7.954  -2.568  -2.964  1.00  0.00           H  
+ATOM    219  HB2 LEU A 138       5.005  -2.464  -3.100  1.00  0.00           H  
+ATOM    220  HB3 LEU A 138       5.778  -1.007  -2.503  1.00  0.00           H  
+ATOM    221  HG  LEU A 138       7.058  -2.000  -4.917  1.00  0.00           H  
+ATOM    222 HD11 LEU A 138       4.115  -1.767  -4.857  1.00  0.00           H  
+ATOM    223 HD12 LEU A 138       4.949  -1.015  -6.216  1.00  0.00           H  
+ATOM    224 HD13 LEU A 138       5.159  -2.737  -5.896  1.00  0.00           H  
+ATOM    225 HD21 LEU A 138       6.904   0.352  -3.631  1.00  0.00           H  
+ATOM    226 HD22 LEU A 138       7.296   0.205  -5.344  1.00  0.00           H  
+ATOM    227 HD23 LEU A 138       5.648   0.590  -4.846  1.00  0.00           H  
+ATOM    228  N   LEU A 139       6.240  -2.853  -0.180  1.00  0.00           N  
+ATOM    229  CA  LEU A 139       6.248  -2.578   1.250  1.00  0.00           C  
+ATOM    230  C   LEU A 139       7.558  -3.027   1.879  1.00  0.00           C  
+ATOM    231  O   LEU A 139       8.099  -2.352   2.755  1.00  0.00           O  
+ATOM    232  CB  LEU A 139       5.069  -3.283   1.932  1.00  0.00           C  
+ATOM    233  CG  LEU A 139       3.756  -2.498   1.970  1.00  0.00           C  
+ATOM    234  CD1 LEU A 139       2.759  -3.172   2.903  1.00  0.00           C  
+ATOM    235  CD2 LEU A 139       3.995  -1.056   2.398  1.00  0.00           C  
+ATOM    236  H   LEU A 139       5.534  -3.417  -0.552  1.00  0.00           H  
+ATOM    237  HA  LEU A 139       6.149  -1.513   1.381  1.00  0.00           H  
+ATOM    238  HB2 LEU A 139       4.882  -4.210   1.409  1.00  0.00           H  
+ATOM    239  HB3 LEU A 139       5.353  -3.515   2.948  1.00  0.00           H  
+ATOM    240  HG  LEU A 139       3.329  -2.489   0.981  1.00  0.00           H  
+ATOM    241 HD11 LEU A 139       3.276  -3.541   3.775  1.00  0.00           H  
+ATOM    242 HD12 LEU A 139       2.009  -2.455   3.205  1.00  0.00           H  
+ATOM    243 HD13 LEU A 139       2.286  -3.995   2.388  1.00  0.00           H  
+ATOM    244 HD21 LEU A 139       4.960  -0.978   2.877  1.00  0.00           H  
+ATOM    245 HD22 LEU A 139       3.971  -0.415   1.531  1.00  0.00           H  
+ATOM    246 HD23 LEU A 139       3.224  -0.752   3.092  1.00  0.00           H  
+ATOM    247  N   ALA A 140       8.056  -4.176   1.433  1.00  0.00           N  
+ATOM    248  CA  ALA A 140       9.303  -4.723   1.959  1.00  0.00           C  
+ATOM    249  C   ALA A 140      10.519  -3.909   1.525  1.00  0.00           C  
+ATOM    250  O   ALA A 140      11.366  -3.561   2.348  1.00  0.00           O  
+ATOM    251  CB  ALA A 140       9.461  -6.176   1.536  1.00  0.00           C  
+ATOM    252  H   ALA A 140       7.566  -4.674   0.738  1.00  0.00           H  
+ATOM    253  HA  ALA A 140       9.242  -4.694   3.032  1.00  0.00           H  
+ATOM    254  HB1 ALA A 140       9.109  -6.297   0.523  1.00  0.00           H  
+ATOM    255  HB2 ALA A 140       8.884  -6.808   2.196  1.00  0.00           H  
+ATOM    256  HB3 ALA A 140      10.503  -6.455   1.592  1.00  0.00           H  
+ATOM    257  N   GLU A 141      10.604  -3.608   0.236  1.00  0.00           N  
+ATOM    258  CA  GLU A 141      11.727  -2.835  -0.291  1.00  0.00           C  
+ATOM    259  C   GLU A 141      11.593  -1.372   0.098  1.00  0.00           C  
+ATOM    260  O   GLU A 141      12.571  -0.716   0.456  1.00  0.00           O  
+ATOM    261  CB  GLU A 141      11.811  -2.952  -1.815  1.00  0.00           C  
+ATOM    262  CG  GLU A 141      11.487  -4.336  -2.340  1.00  0.00           C  
+ATOM    263  CD  GLU A 141      12.352  -5.415  -1.719  1.00  0.00           C  
+ATOM    264  OE1 GLU A 141      11.815  -6.497  -1.402  1.00  0.00           O  
+ATOM    265  OE2 GLU A 141      13.566  -5.178  -1.549  1.00  0.00           O  
+ATOM    266  H   GLU A 141       9.903  -3.909  -0.370  1.00  0.00           H  
+ATOM    267  HA  GLU A 141      12.628  -3.231   0.142  1.00  0.00           H  
+ATOM    268  HB2 GLU A 141      11.116  -2.252  -2.256  1.00  0.00           H  
+ATOM    269  HB3 GLU A 141      12.812  -2.696  -2.128  1.00  0.00           H  
+ATOM    270  HG2 GLU A 141      10.455  -4.551  -2.121  1.00  0.00           H  
+ATOM    271  HG3 GLU A 141      11.636  -4.345  -3.409  1.00  0.00           H  
+ATOM    272  N   TRP A 142      10.370  -0.874   0.025  1.00  0.00           N  
+ATOM    273  CA  TRP A 142      10.084   0.511   0.368  1.00  0.00           C  
+ATOM    274  C   TRP A 142       9.892   0.672   1.877  1.00  0.00           C  
+ATOM    275  O   TRP A 142       9.834   1.792   2.384  1.00  0.00           O  
+ATOM    276  CB  TRP A 142       8.832   0.997  -0.372  1.00  0.00           C  
+ATOM    277  CG  TRP A 142       8.995   1.033  -1.863  1.00  0.00           C  
+ATOM    278  CD1 TRP A 142       9.191  -0.031  -2.697  1.00  0.00           C  
+ATOM    279  CD2 TRP A 142       8.975   2.197  -2.696  1.00  0.00           C  
+ATOM    280  NE1 TRP A 142       9.295   0.401  -3.996  1.00  0.00           N  
+ATOM    281  CE2 TRP A 142       9.164   1.764  -4.022  1.00  0.00           C  
+ATOM    282  CE3 TRP A 142       8.814   3.562  -2.449  1.00  0.00           C  
+ATOM    283  CZ2 TRP A 142       9.197   2.650  -5.096  1.00  0.00           C  
+ATOM    284  CZ3 TRP A 142       8.846   4.441  -3.515  1.00  0.00           C  
+ATOM    285  CH2 TRP A 142       9.037   3.981  -4.825  1.00  0.00           C  
+ATOM    286  H   TRP A 142       9.638  -1.458  -0.270  1.00  0.00           H  
+ATOM    287  HA  TRP A 142      10.928   1.110   0.060  1.00  0.00           H  
+ATOM    288  HB2 TRP A 142       8.008   0.341  -0.143  1.00  0.00           H  
+ATOM    289  HB3 TRP A 142       8.590   1.993  -0.041  1.00  0.00           H  
+ATOM    290  HD1 TRP A 142       9.254  -1.059  -2.370  1.00  0.00           H  
+ATOM    291  HE1 TRP A 142       9.437  -0.173  -4.778  1.00  0.00           H  
+ATOM    292  HE3 TRP A 142       8.667   3.935  -1.446  1.00  0.00           H  
+ATOM    293  HZ2 TRP A 142       9.342   2.313  -6.111  1.00  0.00           H  
+ATOM    294  HZ3 TRP A 142       8.722   5.499  -3.343  1.00  0.00           H  
+ATOM    295  HH2 TRP A 142       9.056   4.704  -5.628  1.00  0.00           H  
+ATOM    296  N   ASN A 143       9.795  -0.452   2.592  1.00  0.00           N  
+ATOM    297  CA  ASN A 143       9.612  -0.422   4.041  1.00  0.00           C  
+ATOM    298  C   ASN A 143       8.482   0.527   4.428  1.00  0.00           C  
+ATOM    299  O   ASN A 143       8.675   1.457   5.210  1.00  0.00           O  
+ATOM    300  CB  ASN A 143      10.912   0.000   4.731  1.00  0.00           C  
+ATOM    301  CG  ASN A 143      11.784  -1.185   5.095  1.00  0.00           C  
+ATOM    302  OD1 ASN A 143      11.312  -2.321   5.164  1.00  0.00           O  
+ATOM    303  ND2 ASN A 143      13.065  -0.927   5.332  1.00  0.00           N  
+ATOM    304  H   ASN A 143       9.849  -1.320   2.139  1.00  0.00           H  
+ATOM    305  HA  ASN A 143       9.354  -1.420   4.362  1.00  0.00           H  
+ATOM    306  HB2 ASN A 143      11.471   0.644   4.069  1.00  0.00           H  
+ATOM    307  HB3 ASN A 143      10.673   0.540   5.635  1.00  0.00           H  
+ATOM    308 HD21 ASN A 143      13.371   0.001   5.259  1.00  0.00           H  
+ATOM    309 HD22 ASN A 143      13.652  -1.675   5.569  1.00  0.00           H  
+ATOM    310  N   LEU A 144       7.301   0.286   3.868  1.00  0.00           N  
+ATOM    311  CA  LEU A 144       6.140   1.121   4.150  1.00  0.00           C  
+ATOM    312  C   LEU A 144       5.147   0.395   5.053  1.00  0.00           C  
+ATOM    313  O   LEU A 144       5.117  -0.834   5.098  1.00  0.00           O  
+ATOM    314  CB  LEU A 144       5.455   1.535   2.845  1.00  0.00           C  
+ATOM    315  CG  LEU A 144       5.921   2.870   2.263  1.00  0.00           C  
+ATOM    316  CD1 LEU A 144       5.241   3.137   0.929  1.00  0.00           C  
+ATOM    317  CD2 LEU A 144       5.644   4.004   3.239  1.00  0.00           C  
+ATOM    318  H   LEU A 144       7.211  -0.472   3.250  1.00  0.00           H  
+ATOM    319  HA  LEU A 144       6.486   2.008   4.659  1.00  0.00           H  
+ATOM    320  HB2 LEU A 144       5.635   0.764   2.110  1.00  0.00           H  
+ATOM    321  HB3 LEU A 144       4.392   1.598   3.024  1.00  0.00           H  
+ATOM    322  HG  LEU A 144       6.987   2.828   2.092  1.00  0.00           H  
+ATOM    323 HD11 LEU A 144       4.296   2.614   0.896  1.00  0.00           H  
+ATOM    324 HD12 LEU A 144       5.070   4.197   0.818  1.00  0.00           H  
+ATOM    325 HD13 LEU A 144       5.874   2.787   0.127  1.00  0.00           H  
+ATOM    326 HD21 LEU A 144       4.802   3.744   3.863  1.00  0.00           H  
+ATOM    327 HD22 LEU A 144       6.515   4.168   3.856  1.00  0.00           H  
+ATOM    328 HD23 LEU A 144       5.419   4.906   2.687  1.00  0.00           H  
+ATOM    329  N   ASP A 145       4.337   1.166   5.772  1.00  0.00           N  
+ATOM    330  CA  ASP A 145       3.342   0.599   6.673  1.00  0.00           C  
+ATOM    331  C   ASP A 145       1.935   0.797   6.117  1.00  0.00           C  
+ATOM    332  O   ASP A 145       1.444   1.922   6.030  1.00  0.00           O  
+ATOM    333  CB  ASP A 145       3.451   1.241   8.057  1.00  0.00           C  
+ATOM    334  CG  ASP A 145       3.205   0.247   9.177  1.00  0.00           C  
+ATOM    335  OD1 ASP A 145       2.727   0.669  10.250  1.00  0.00           O  
+ATOM    336  OD2 ASP A 145       3.490  -0.953   8.978  1.00  0.00           O  
+ATOM    337  H   ASP A 145       4.409   2.140   5.692  1.00  0.00           H  
+ATOM    338  HA  ASP A 145       3.537  -0.460   6.759  1.00  0.00           H  
+ATOM    339  HB2 ASP A 145       4.442   1.652   8.179  1.00  0.00           H  
+ATOM    340  HB3 ASP A 145       2.723   2.034   8.138  1.00  0.00           H  
+ATOM    341  N   ALA A 146       1.293  -0.304   5.741  1.00  0.00           N  
+ATOM    342  CA  ALA A 146      -0.055  -0.251   5.190  1.00  0.00           C  
+ATOM    343  C   ALA A 146      -1.031   0.376   6.180  1.00  0.00           C  
+ATOM    344  O   ALA A 146      -1.961   1.083   5.788  1.00  0.00           O  
+ATOM    345  CB  ALA A 146      -0.520  -1.646   4.802  1.00  0.00           C  
+ATOM    346  H   ALA A 146       1.738  -1.172   5.832  1.00  0.00           H  
+ATOM    347  HA  ALA A 146      -0.026   0.354   4.296  1.00  0.00           H  
+ATOM    348  HB1 ALA A 146      -0.232  -2.347   5.571  1.00  0.00           H  
+ATOM    349  HB2 ALA A 146      -1.595  -1.650   4.696  1.00  0.00           H  
+ATOM    350  HB3 ALA A 146      -0.064  -1.929   3.865  1.00  0.00           H  
+ATOM    351  N   SER A 147      -0.814   0.112   7.463  1.00  0.00           N  
+ATOM    352  CA  SER A 147      -1.675   0.647   8.511  1.00  0.00           C  
+ATOM    353  C   SER A 147      -1.648   2.173   8.515  1.00  0.00           C  
+ATOM    354  O   SER A 147      -2.632   2.820   8.873  1.00  0.00           O  
+ATOM    355  CB  SER A 147      -1.240   0.115   9.877  1.00  0.00           C  
+ATOM    356  OG  SER A 147       0.067   0.557  10.204  1.00  0.00           O  
+ATOM    357  H   SER A 147      -0.058  -0.459   7.711  1.00  0.00           H  
+ATOM    358  HA  SER A 147      -2.683   0.318   8.312  1.00  0.00           H  
+ATOM    359  HB2 SER A 147      -1.925   0.469  10.634  1.00  0.00           H  
+ATOM    360  HB3 SER A 147      -1.249  -0.964   9.860  1.00  0.00           H  
+ATOM    361  HG  SER A 147       0.018   1.205  10.911  1.00  0.00           H  
+ATOM    362  N   ALA A 148      -0.515   2.742   8.116  1.00  0.00           N  
+ATOM    363  CA  ALA A 148      -0.361   4.191   8.075  1.00  0.00           C  
+ATOM    364  C   ALA A 148      -0.604   4.740   6.671  1.00  0.00           C  
+ATOM    365  O   ALA A 148      -0.231   5.874   6.369  1.00  0.00           O  
+ATOM    366  CB  ALA A 148       1.024   4.586   8.565  1.00  0.00           C  
+ATOM    367  H   ALA A 148       0.236   2.174   7.842  1.00  0.00           H  
+ATOM    368  HA  ALA A 148      -1.089   4.620   8.749  1.00  0.00           H  
+ATOM    369  HB1 ALA A 148       1.263   4.026   9.457  1.00  0.00           H  
+ATOM    370  HB2 ALA A 148       1.039   5.643   8.788  1.00  0.00           H  
+ATOM    371  HB3 ALA A 148       1.752   4.369   7.797  1.00  0.00           H  
+ATOM    372  N   ILE A 149      -1.228   3.935   5.816  1.00  0.00           N  
+ATOM    373  CA  ILE A 149      -1.514   4.350   4.448  1.00  0.00           C  
+ATOM    374  C   ILE A 149      -2.976   4.095   4.092  1.00  0.00           C  
+ATOM    375  O   ILE A 149      -3.486   2.990   4.276  1.00  0.00           O  
+ATOM    376  CB  ILE A 149      -0.614   3.613   3.436  1.00  0.00           C  
+ATOM    377  CG1 ILE A 149       0.856   3.738   3.841  1.00  0.00           C  
+ATOM    378  CG2 ILE A 149      -0.828   4.164   2.034  1.00  0.00           C  
+ATOM    379  CD1 ILE A 149       1.711   2.578   3.380  1.00  0.00           C  
+ATOM    380  H   ILE A 149      -1.502   3.042   6.111  1.00  0.00           H  
+ATOM    381  HA  ILE A 149      -1.315   5.409   4.373  1.00  0.00           H  
+ATOM    382  HB  ILE A 149      -0.891   2.570   3.433  1.00  0.00           H  
+ATOM    383 HG12 ILE A 149       1.266   4.641   3.413  1.00  0.00           H  
+ATOM    384 HG13 ILE A 149       0.923   3.793   4.918  1.00  0.00           H  
+ATOM    385 HG21 ILE A 149      -1.115   5.204   2.095  1.00  0.00           H  
+ATOM    386 HG22 ILE A 149       0.086   4.075   1.468  1.00  0.00           H  
+ATOM    387 HG23 ILE A 149      -1.611   3.603   1.543  1.00  0.00           H  
+ATOM    388 HD11 ILE A 149       1.100   1.691   3.297  1.00  0.00           H  
+ATOM    389 HD12 ILE A 149       2.141   2.809   2.416  1.00  0.00           H  
+ATOM    390 HD13 ILE A 149       2.501   2.406   4.095  1.00  0.00           H  
+ATOM    391  N   LYS A 150      -3.642   5.125   3.580  1.00  0.00           N  
+ATOM    392  CA  LYS A 150      -5.045   5.012   3.198  1.00  0.00           C  
+ATOM    393  C   LYS A 150      -5.187   4.322   1.846  1.00  0.00           C  
+ATOM    394  O   LYS A 150      -4.365   4.514   0.951  1.00  0.00           O  
+ATOM    395  CB  LYS A 150      -5.693   6.397   3.147  1.00  0.00           C  
+ATOM    396  CG  LYS A 150      -7.171   6.391   3.501  1.00  0.00           C  
+ATOM    397  CD  LYS A 150      -7.386   6.238   5.000  1.00  0.00           C  
+ATOM    398  CE  LYS A 150      -8.316   7.311   5.543  1.00  0.00           C  
+ATOM    399  NZ  LYS A 150      -8.889   6.933   6.865  1.00  0.00           N  
+ATOM    400  H   LYS A 150      -3.180   5.980   3.457  1.00  0.00           H  
+ATOM    401  HA  LYS A 150      -5.546   4.418   3.947  1.00  0.00           H  
+ATOM    402  HB2 LYS A 150      -5.181   7.048   3.840  1.00  0.00           H  
+ATOM    403  HB3 LYS A 150      -5.586   6.795   2.148  1.00  0.00           H  
+ATOM    404  HG2 LYS A 150      -7.613   7.322   3.177  1.00  0.00           H  
+ATOM    405  HG3 LYS A 150      -7.650   5.567   2.993  1.00  0.00           H  
+ATOM    406  HD2 LYS A 150      -7.819   5.270   5.195  1.00  0.00           H  
+ATOM    407  HD3 LYS A 150      -6.432   6.315   5.501  1.00  0.00           H  
+ATOM    408  HE2 LYS A 150      -7.761   8.230   5.653  1.00  0.00           H  
+ATOM    409  HE3 LYS A 150      -9.122   7.460   4.840  1.00  0.00           H  
+ATOM    410  HZ1 LYS A 150      -8.209   6.352   7.396  1.00  0.00           H  
+ATOM    411  HZ2 LYS A 150      -9.107   7.786   7.419  1.00  0.00           H  
+ATOM    412  HZ3 LYS A 150      -9.765   6.387   6.732  1.00  0.00           H  
+ATOM    413  N   GLY A 151      -6.234   3.517   1.706  1.00  0.00           N  
+ATOM    414  CA  GLY A 151      -6.464   2.809   0.459  1.00  0.00           C  
+ATOM    415  C   GLY A 151      -7.936   2.553   0.200  1.00  0.00           C  
+ATOM    416  O   GLY A 151      -8.796   3.022   0.945  1.00  0.00           O  
+ATOM    417  H   GLY A 151      -6.857   3.401   2.453  1.00  0.00           H  
+ATOM    418  HA2 GLY A 151      -6.064   3.396  -0.354  1.00  0.00           H  
+ATOM    419  HA3 GLY A 151      -5.946   1.863   0.496  1.00  0.00           H  
+ATOM    420  N   THR A 152      -8.227   1.805  -0.860  1.00  0.00           N  
+ATOM    421  CA  THR A 152      -9.604   1.487  -1.216  1.00  0.00           C  
+ATOM    422  C   THR A 152      -9.655   0.373  -2.258  1.00  0.00           C  
+ATOM    423  O   THR A 152      -9.911   0.622  -3.436  1.00  0.00           O  
+ATOM    424  CB  THR A 152     -10.316   2.732  -1.748  1.00  0.00           C  
+ATOM    425  OG1 THR A 152     -11.652   2.429  -2.111  1.00  0.00           O  
+ATOM    426  CG2 THR A 152      -9.638   3.337  -2.958  1.00  0.00           C  
+ATOM    427  H   THR A 152      -7.497   1.459  -1.417  1.00  0.00           H  
+ATOM    428  HA  THR A 152     -10.107   1.150  -0.322  1.00  0.00           H  
+ATOM    429  HB  THR A 152     -10.336   3.482  -0.970  1.00  0.00           H  
+ATOM    430  HG1 THR A 152     -11.652   1.776  -2.814  1.00  0.00           H  
+ATOM    431 HG21 THR A 152      -8.686   2.852  -3.117  1.00  0.00           H  
+ATOM    432 HG22 THR A 152     -10.262   3.198  -3.828  1.00  0.00           H  
+ATOM    433 HG23 THR A 152      -9.480   4.393  -2.792  1.00  0.00           H  
+ATOM    434  N   GLY A 153      -9.409  -0.856  -1.814  1.00  0.00           N  
+ATOM    435  CA  GLY A 153      -9.432  -1.990  -2.720  1.00  0.00           C  
+ATOM    436  C   GLY A 153     -10.647  -2.873  -2.512  1.00  0.00           C  
+ATOM    437  O   GLY A 153     -11.397  -3.139  -3.451  1.00  0.00           O  
+ATOM    438  H   GLY A 153      -9.211  -0.994  -0.865  1.00  0.00           H  
+ATOM    439  HA2 GLY A 153      -9.436  -1.625  -3.736  1.00  0.00           H  
+ATOM    440  HA3 GLY A 153      -8.540  -2.579  -2.564  1.00  0.00           H  
+ATOM    441  N   VAL A 154     -10.839  -3.328  -1.279  1.00  0.00           N  
+ATOM    442  CA  VAL A 154     -11.971  -4.188  -0.949  1.00  0.00           C  
+ATOM    443  C   VAL A 154     -12.485  -3.896   0.457  1.00  0.00           C  
+ATOM    444  O   VAL A 154     -12.857  -4.807   1.197  1.00  0.00           O  
+ATOM    445  CB  VAL A 154     -11.594  -5.679  -1.048  1.00  0.00           C  
+ATOM    446  CG1 VAL A 154     -12.836  -6.552  -0.954  1.00  0.00           C  
+ATOM    447  CG2 VAL A 154     -10.836  -5.954  -2.338  1.00  0.00           C  
+ATOM    448  H   VAL A 154     -10.205  -3.081  -0.574  1.00  0.00           H  
+ATOM    449  HA  VAL A 154     -12.759  -3.987  -1.659  1.00  0.00           H  
+ATOM    450  HB  VAL A 154     -10.947  -5.922  -0.217  1.00  0.00           H  
+ATOM    451 HG11 VAL A 154     -13.650  -5.978  -0.539  1.00  0.00           H  
+ATOM    452 HG12 VAL A 154     -13.106  -6.901  -1.939  1.00  0.00           H  
+ATOM    453 HG13 VAL A 154     -12.632  -7.399  -0.315  1.00  0.00           H  
+ATOM    454 HG21 VAL A 154      -9.989  -5.288  -2.407  1.00  0.00           H  
+ATOM    455 HG22 VAL A 154     -10.490  -6.977  -2.340  1.00  0.00           H  
+ATOM    456 HG23 VAL A 154     -11.491  -5.793  -3.182  1.00  0.00           H  
+ATOM    457  N   GLY A 155     -12.501  -2.617   0.821  1.00  0.00           N  
+ATOM    458  CA  GLY A 155     -12.970  -2.226   2.137  1.00  0.00           C  
+ATOM    459  C   GLY A 155     -11.832  -1.859   3.070  1.00  0.00           C  
+ATOM    460  O   GLY A 155     -12.006  -1.059   3.989  1.00  0.00           O  
+ATOM    461  H   GLY A 155     -12.193  -1.934   0.191  1.00  0.00           H  
+ATOM    462  HA2 GLY A 155     -13.627  -1.375   2.036  1.00  0.00           H  
+ATOM    463  HA3 GLY A 155     -13.524  -3.047   2.569  1.00  0.00           H  
+ATOM    464  N   GLY A 156     -10.663  -2.448   2.833  1.00  0.00           N  
+ATOM    465  CA  GLY A 156      -9.509  -2.166   3.664  1.00  0.00           C  
+ATOM    466  C   GLY A 156      -8.214  -2.641   3.033  1.00  0.00           C  
+ATOM    467  O   GLY A 156      -7.546  -3.528   3.564  1.00  0.00           O  
+ATOM    468  H   GLY A 156     -10.586  -3.076   2.085  1.00  0.00           H  
+ATOM    469  HA2 GLY A 156      -9.447  -1.101   3.828  1.00  0.00           H  
+ATOM    470  HA3 GLY A 156      -9.635  -2.661   4.615  1.00  0.00           H  
+ATOM    471  N   ARG A 157      -7.860  -2.050   1.896  1.00  0.00           N  
+ATOM    472  CA  ARG A 157      -6.638  -2.418   1.189  1.00  0.00           C  
+ATOM    473  C   ARG A 157      -6.072  -1.227   0.426  1.00  0.00           C  
+ATOM    474  O   ARG A 157      -6.821  -0.391  -0.080  1.00  0.00           O  
+ATOM    475  CB  ARG A 157      -6.914  -3.567   0.218  1.00  0.00           C  
+ATOM    476  CG  ARG A 157      -7.078  -4.917   0.897  1.00  0.00           C  
+ATOM    477  CD  ARG A 157      -7.586  -5.970  -0.074  1.00  0.00           C  
+ATOM    478  NE  ARG A 157      -6.508  -6.524  -0.891  1.00  0.00           N  
+ATOM    479  CZ  ARG A 157      -6.578  -7.697  -1.518  1.00  0.00           C  
+ATOM    480  NH1 ARG A 157      -7.674  -8.442  -1.428  1.00  0.00           N  
+ATOM    481  NH2 ARG A 157      -5.550  -8.127  -2.237  1.00  0.00           N  
+ATOM    482  H   ARG A 157      -8.436  -1.350   1.522  1.00  0.00           H  
+ATOM    483  HA  ARG A 157      -5.916  -2.741   1.922  1.00  0.00           H  
+ATOM    484  HB2 ARG A 157      -7.821  -3.352  -0.328  1.00  0.00           H  
+ATOM    485  HB3 ARG A 157      -6.093  -3.637  -0.480  1.00  0.00           H  
+ATOM    486  HG2 ARG A 157      -6.121  -5.231   1.283  1.00  0.00           H  
+ATOM    487  HG3 ARG A 157      -7.782  -4.818   1.709  1.00  0.00           H  
+ATOM    488  HD2 ARG A 157      -8.044  -6.769   0.489  1.00  0.00           H  
+ATOM    489  HD3 ARG A 157      -8.321  -5.519  -0.723  1.00  0.00           H  
+ATOM    490  HE  ARG A 157      -5.687  -5.995  -0.977  1.00  0.00           H  
+ATOM    491 HH11 ARG A 157      -8.453  -8.124  -0.888  1.00  0.00           H  
+ATOM    492 HH12 ARG A 157      -7.720  -9.321  -1.902  1.00  0.00           H  
+ATOM    493 HH21 ARG A 157      -4.723  -7.570  -2.309  1.00  0.00           H  
+ATOM    494 HH22 ARG A 157      -5.603  -9.007  -2.707  1.00  0.00           H  
+ATOM    495  N   LEU A 158      -4.746  -1.155   0.336  1.00  0.00           N  
+ATOM    496  CA  LEU A 158      -4.093  -0.068  -0.380  1.00  0.00           C  
+ATOM    497  C   LEU A 158      -3.454  -0.604  -1.661  1.00  0.00           C  
+ATOM    498  O   LEU A 158      -2.802  -1.648  -1.649  1.00  0.00           O  
+ATOM    499  CB  LEU A 158      -3.074   0.619   0.553  1.00  0.00           C  
+ATOM    500  CG  LEU A 158      -1.625   0.711   0.059  1.00  0.00           C  
+ATOM    501  CD1 LEU A 158      -1.378   2.051  -0.615  1.00  0.00           C  
+ATOM    502  CD2 LEU A 158      -0.658   0.522   1.220  1.00  0.00           C  
+ATOM    503  H   LEU A 158      -4.193  -1.854   0.751  1.00  0.00           H  
+ATOM    504  HA  LEU A 158      -4.857   0.648  -0.651  1.00  0.00           H  
+ATOM    505  HB2 LEU A 158      -3.422   1.624   0.739  1.00  0.00           H  
+ATOM    506  HB3 LEU A 158      -3.073   0.085   1.491  1.00  0.00           H  
+ATOM    507  HG  LEU A 158      -1.440  -0.072  -0.661  1.00  0.00           H  
+ATOM    508 HD11 LEU A 158      -2.095   2.772  -0.254  1.00  0.00           H  
+ATOM    509 HD12 LEU A 158      -0.379   2.390  -0.384  1.00  0.00           H  
+ATOM    510 HD13 LEU A 158      -1.481   1.941  -1.682  1.00  0.00           H  
+ATOM    511 HD21 LEU A 158      -1.153  -0.008   2.019  1.00  0.00           H  
+ATOM    512 HD22 LEU A 158       0.198  -0.046   0.886  1.00  0.00           H  
+ATOM    513 HD23 LEU A 158      -0.332   1.488   1.578  1.00  0.00           H  
+ATOM    514  N   THR A 159      -3.669   0.100  -2.770  1.00  0.00           N  
+ATOM    515  CA  THR A 159      -3.138  -0.329  -4.064  1.00  0.00           C  
+ATOM    516  C   THR A 159      -1.926   0.498  -4.478  1.00  0.00           C  
+ATOM    517  O   THR A 159      -1.539   1.434  -3.784  1.00  0.00           O  
+ATOM    518  CB  THR A 159      -4.224  -0.242  -5.134  1.00  0.00           C  
+ATOM    519  OG1 THR A 159      -4.432   1.100  -5.533  1.00  0.00           O  
+ATOM    520  CG2 THR A 159      -5.554  -0.796  -4.671  1.00  0.00           C  
+ATOM    521  H   THR A 159      -4.215   0.913  -2.724  1.00  0.00           H  
+ATOM    522  HA  THR A 159      -2.831  -1.360  -3.965  1.00  0.00           H  
+ATOM    523  HB  THR A 159      -3.912  -0.810  -5.999  1.00  0.00           H  
+ATOM    524  HG1 THR A 159      -4.724   1.617  -4.778  1.00  0.00           H  
+ATOM    525 HG21 THR A 159      -5.481  -1.088  -3.634  1.00  0.00           H  
+ATOM    526 HG22 THR A 159      -6.317  -0.039  -4.780  1.00  0.00           H  
+ATOM    527 HG23 THR A 159      -5.813  -1.657  -5.270  1.00  0.00           H  
+ATOM    528  N   ARG A 160      -1.335   0.139  -5.619  1.00  0.00           N  
+ATOM    529  CA  ARG A 160      -0.152   0.830  -6.129  1.00  0.00           C  
+ATOM    530  C   ARG A 160      -0.413   2.322  -6.283  1.00  0.00           C  
+ATOM    531  O   ARG A 160       0.491   3.139  -6.108  1.00  0.00           O  
+ATOM    532  CB  ARG A 160       0.260   0.237  -7.477  1.00  0.00           C  
+ATOM    533  CG  ARG A 160      -0.772   0.442  -8.574  1.00  0.00           C  
+ATOM    534  CD  ARG A 160      -0.394  -0.304  -9.844  1.00  0.00           C  
+ATOM    535  NE  ARG A 160      -1.385  -0.124 -10.901  1.00  0.00           N  
+ATOM    536  CZ  ARG A 160      -1.558   1.015 -11.571  1.00  0.00           C  
+ATOM    537  NH1 ARG A 160      -0.810   2.075 -11.295  1.00  0.00           N  
+ATOM    538  NH2 ARG A 160      -2.483   1.092 -12.518  1.00  0.00           N  
+ATOM    539  H   ARG A 160      -1.697  -0.619  -6.123  1.00  0.00           H  
+ATOM    540  HA  ARG A 160       0.652   0.685  -5.424  1.00  0.00           H  
+ATOM    541  HB2 ARG A 160       1.184   0.699  -7.792  1.00  0.00           H  
+ATOM    542  HB3 ARG A 160       0.420  -0.824  -7.357  1.00  0.00           H  
+ATOM    543  HG2 ARG A 160      -1.728   0.079  -8.228  1.00  0.00           H  
+ATOM    544  HG3 ARG A 160      -0.844   1.498  -8.795  1.00  0.00           H  
+ATOM    545  HD2 ARG A 160       0.560   0.066 -10.192  1.00  0.00           H  
+ATOM    546  HD3 ARG A 160      -0.309  -1.356  -9.617  1.00  0.00           H  
+ATOM    547  HE  ARG A 160      -1.952  -0.891 -11.125  1.00  0.00           H  
+ATOM    548 HH11 ARG A 160      -0.111   2.024 -10.582  1.00  0.00           H  
+ATOM    549 HH12 ARG A 160      -0.944   2.927 -11.801  1.00  0.00           H  
+ATOM    550 HH21 ARG A 160      -3.050   0.296 -12.730  1.00  0.00           H  
+ATOM    551 HH22 ARG A 160      -2.613   1.946 -13.020  1.00  0.00           H  
+ATOM    552  N   GLU A 161      -1.651   2.676  -6.592  1.00  0.00           N  
+ATOM    553  CA  GLU A 161      -2.017   4.075  -6.743  1.00  0.00           C  
+ATOM    554  C   GLU A 161      -2.089   4.743  -5.374  1.00  0.00           C  
+ATOM    555  O   GLU A 161      -1.765   5.923  -5.221  1.00  0.00           O  
+ATOM    556  CB  GLU A 161      -3.352   4.214  -7.482  1.00  0.00           C  
+ATOM    557  CG  GLU A 161      -4.562   3.781  -6.668  1.00  0.00           C  
+ATOM    558  CD  GLU A 161      -5.480   2.849  -7.434  1.00  0.00           C  
+ATOM    559  OE1 GLU A 161      -4.974   1.874  -8.028  1.00  0.00           O  
+ATOM    560  OE2 GLU A 161      -6.705   3.093  -7.439  1.00  0.00           O  
+ATOM    561  H   GLU A 161      -2.335   1.984  -6.706  1.00  0.00           H  
+ATOM    562  HA  GLU A 161      -1.241   4.556  -7.319  1.00  0.00           H  
+ATOM    563  HB2 GLU A 161      -3.488   5.248  -7.762  1.00  0.00           H  
+ATOM    564  HB3 GLU A 161      -3.315   3.611  -8.378  1.00  0.00           H  
+ATOM    565  HG2 GLU A 161      -4.220   3.275  -5.780  1.00  0.00           H  
+ATOM    566  HG3 GLU A 161      -5.121   4.661  -6.384  1.00  0.00           H  
+ATOM    567  N   ASP A 162      -2.509   3.973  -4.375  1.00  0.00           N  
+ATOM    568  CA  ASP A 162      -2.616   4.483  -3.017  1.00  0.00           C  
+ATOM    569  C   ASP A 162      -1.233   4.615  -2.390  1.00  0.00           C  
+ATOM    570  O   ASP A 162      -0.984   5.530  -1.602  1.00  0.00           O  
+ATOM    571  CB  ASP A 162      -3.502   3.566  -2.171  1.00  0.00           C  
+ATOM    572  CG  ASP A 162      -4.957   3.622  -2.588  1.00  0.00           C  
+ATOM    573  OD1 ASP A 162      -5.525   4.735  -2.613  1.00  0.00           O  
+ATOM    574  OD2 ASP A 162      -5.530   2.554  -2.890  1.00  0.00           O  
+ATOM    575  H   ASP A 162      -2.742   3.037  -4.554  1.00  0.00           H  
+ATOM    576  HA  ASP A 162      -3.070   5.461  -3.067  1.00  0.00           H  
+ATOM    577  HB2 ASP A 162      -3.159   2.548  -2.276  1.00  0.00           H  
+ATOM    578  HB3 ASP A 162      -3.431   3.862  -1.135  1.00  0.00           H  
+ATOM    579  N   VAL A 163      -0.326   3.711  -2.756  1.00  0.00           N  
+ATOM    580  CA  VAL A 163       1.035   3.759  -2.227  1.00  0.00           C  
+ATOM    581  C   VAL A 163       1.798   4.903  -2.876  1.00  0.00           C  
+ATOM    582  O   VAL A 163       2.469   5.673  -2.195  1.00  0.00           O  
+ATOM    583  CB  VAL A 163       1.842   2.448  -2.438  1.00  0.00           C  
+ATOM    584  CG1 VAL A 163       2.572   2.067  -1.161  1.00  0.00           C  
+ATOM    585  CG2 VAL A 163       0.966   1.302  -2.901  1.00  0.00           C  
+ATOM    586  H   VAL A 163      -0.574   3.016  -3.398  1.00  0.00           H  
+ATOM    587  HA  VAL A 163       0.966   3.950  -1.164  1.00  0.00           H  
+ATOM    588  HB  VAL A 163       2.584   2.629  -3.203  1.00  0.00           H  
+ATOM    589 HG11 VAL A 163       2.808   2.959  -0.600  1.00  0.00           H  
+ATOM    590 HG12 VAL A 163       1.937   1.423  -0.566  1.00  0.00           H  
+ATOM    591 HG13 VAL A 163       3.483   1.546  -1.410  1.00  0.00           H  
+ATOM    592 HG21 VAL A 163       0.200   1.111  -2.167  1.00  0.00           H  
+ATOM    593 HG22 VAL A 163       0.512   1.561  -3.840  1.00  0.00           H  
+ATOM    594 HG23 VAL A 163       1.571   0.417  -3.027  1.00  0.00           H  
+ATOM    595  N   GLU A 164       1.683   5.022  -4.199  1.00  0.00           N  
+ATOM    596  CA  GLU A 164       2.361   6.090  -4.920  1.00  0.00           C  
+ATOM    597  C   GLU A 164       1.890   7.442  -4.403  1.00  0.00           C  
+ATOM    598  O   GLU A 164       2.691   8.352  -4.188  1.00  0.00           O  
+ATOM    599  CB  GLU A 164       2.117   5.973  -6.428  1.00  0.00           C  
+ATOM    600  CG  GLU A 164       0.714   6.371  -6.855  1.00  0.00           C  
+ATOM    601  CD  GLU A 164       0.527   6.326  -8.358  1.00  0.00           C  
+ATOM    602  OE1 GLU A 164       1.001   5.355  -8.986  1.00  0.00           O  
+ATOM    603  OE2 GLU A 164      -0.092   7.260  -8.908  1.00  0.00           O  
+ATOM    604  H   GLU A 164       1.122   4.385  -4.696  1.00  0.00           H  
+ATOM    605  HA  GLU A 164       3.418   5.997  -4.726  1.00  0.00           H  
+ATOM    606  HB2 GLU A 164       2.819   6.610  -6.944  1.00  0.00           H  
+ATOM    607  HB3 GLU A 164       2.284   4.949  -6.728  1.00  0.00           H  
+ATOM    608  HG2 GLU A 164       0.011   5.694  -6.400  1.00  0.00           H  
+ATOM    609  HG3 GLU A 164       0.520   7.376  -6.512  1.00  0.00           H  
+ATOM    610  N   LYS A 165       0.584   7.558  -4.183  1.00  0.00           N  
+ATOM    611  CA  LYS A 165       0.009   8.790  -3.664  1.00  0.00           C  
+ATOM    612  C   LYS A 165       0.561   9.067  -2.271  1.00  0.00           C  
+ATOM    613  O   LYS A 165       0.889  10.203  -1.932  1.00  0.00           O  
+ATOM    614  CB  LYS A 165      -1.517   8.692  -3.618  1.00  0.00           C  
+ATOM    615  CG  LYS A 165      -2.181   8.866  -4.973  1.00  0.00           C  
+ATOM    616  CD  LYS A 165      -2.189  10.322  -5.407  1.00  0.00           C  
+ATOM    617  CE  LYS A 165      -3.262  10.586  -6.450  1.00  0.00           C  
+ATOM    618  NZ  LYS A 165      -4.630  10.536  -5.864  1.00  0.00           N  
+ATOM    619  H   LYS A 165      -0.002   6.790  -4.360  1.00  0.00           H  
+ATOM    620  HA  LYS A 165       0.295   9.597  -4.322  1.00  0.00           H  
+ATOM    621  HB2 LYS A 165      -1.792   7.722  -3.228  1.00  0.00           H  
+ATOM    622  HB3 LYS A 165      -1.896   9.456  -2.955  1.00  0.00           H  
+ATOM    623  HG2 LYS A 165      -1.639   8.286  -5.706  1.00  0.00           H  
+ATOM    624  HG3 LYS A 165      -3.199   8.512  -4.913  1.00  0.00           H  
+ATOM    625  HD2 LYS A 165      -2.378  10.944  -4.545  1.00  0.00           H  
+ATOM    626  HD3 LYS A 165      -1.224  10.569  -5.825  1.00  0.00           H  
+ATOM    627  HE2 LYS A 165      -3.100  11.566  -6.876  1.00  0.00           H  
+ATOM    628  HE3 LYS A 165      -3.184   9.839  -7.225  1.00  0.00           H  
+ATOM    629  HZ1 LYS A 165      -4.618  10.909  -4.894  1.00  0.00           H  
+ATOM    630  HZ2 LYS A 165      -5.286  11.109  -6.434  1.00  0.00           H  
+ATOM    631  HZ3 LYS A 165      -4.974   9.555  -5.842  1.00  0.00           H  
+ATOM    632  N   HIS A 166       0.670   8.007  -1.476  1.00  0.00           N  
+ATOM    633  CA  HIS A 166       1.197   8.110  -0.121  1.00  0.00           C  
+ATOM    634  C   HIS A 166       2.704   8.346  -0.154  1.00  0.00           C  
+ATOM    635  O   HIS A 166       3.256   9.044   0.695  1.00  0.00           O  
+ATOM    636  CB  HIS A 166       0.890   6.831   0.662  1.00  0.00           C  
+ATOM    637  CG  HIS A 166       1.430   6.838   2.059  1.00  0.00           C  
+ATOM    638  ND1 HIS A 166       0.669   7.170   3.160  1.00  0.00           N  
+ATOM    639  CD2 HIS A 166       2.665   6.549   2.531  1.00  0.00           C  
+ATOM    640  CE1 HIS A 166       1.414   7.087   4.249  1.00  0.00           C  
+ATOM    641  NE2 HIS A 166       2.629   6.712   3.894  1.00  0.00           N  
+ATOM    642  H   HIS A 166       0.398   7.128  -1.816  1.00  0.00           H  
+ATOM    643  HA  HIS A 166       0.719   8.947   0.363  1.00  0.00           H  
+ATOM    644  HB2 HIS A 166      -0.179   6.697   0.719  1.00  0.00           H  
+ATOM    645  HB3 HIS A 166       1.324   5.989   0.143  1.00  0.00           H  
+ATOM    646  HD1 HIS A 166      -0.276   7.429   3.146  1.00  0.00           H  
+ATOM    647  HD2 HIS A 166       3.522   6.247   1.945  1.00  0.00           H  
+ATOM    648  HE1 HIS A 166       1.085   7.292   5.256  1.00  0.00           H  
+ATOM    649  HE2 HIS A 166       3.350   6.479   4.514  1.00  0.00           H  
+ATOM    650  N   LEU A 167       3.358   7.748  -1.144  1.00  0.00           N  
+ATOM    651  CA  LEU A 167       4.801   7.874  -1.308  1.00  0.00           C  
+ATOM    652  C   LEU A 167       5.206   9.336  -1.464  1.00  0.00           C  
+ATOM    653  O   LEU A 167       6.299   9.735  -1.062  1.00  0.00           O  
+ATOM    654  CB  LEU A 167       5.261   7.070  -2.526  1.00  0.00           C  
+ATOM    655  CG  LEU A 167       5.466   5.572  -2.279  1.00  0.00           C  
+ATOM    656  CD1 LEU A 167       5.894   4.876  -3.562  1.00  0.00           C  
+ATOM    657  CD2 LEU A 167       6.495   5.349  -1.181  1.00  0.00           C  
+ATOM    658  H   LEU A 167       2.855   7.205  -1.784  1.00  0.00           H  
+ATOM    659  HA  LEU A 167       5.272   7.474  -0.423  1.00  0.00           H  
+ATOM    660  HB2 LEU A 167       4.522   7.186  -3.307  1.00  0.00           H  
+ATOM    661  HB3 LEU A 167       6.196   7.486  -2.874  1.00  0.00           H  
+ATOM    662  HG  LEU A 167       4.531   5.134  -1.959  1.00  0.00           H  
+ATOM    663 HD11 LEU A 167       6.585   5.507  -4.101  1.00  0.00           H  
+ATOM    664 HD12 LEU A 167       6.374   3.940  -3.320  1.00  0.00           H  
+ATOM    665 HD13 LEU A 167       5.025   4.687  -4.175  1.00  0.00           H  
+ATOM    666 HD21 LEU A 167       7.387   5.917  -1.402  1.00  0.00           H  
+ATOM    667 HD22 LEU A 167       6.088   5.674  -0.235  1.00  0.00           H  
+ATOM    668 HD23 LEU A 167       6.740   4.299  -1.126  1.00  0.00           H  
+ATOM    669  N   ALA A 168       4.318  10.130  -2.051  1.00  0.00           N  
+ATOM    670  CA  ALA A 168       4.582  11.549  -2.261  1.00  0.00           C  
+ATOM    671  C   ALA A 168       4.171  12.370  -1.042  1.00  0.00           C  
+ATOM    672  O   ALA A 168       4.749  13.421  -0.767  1.00  0.00           O  
+ATOM    673  CB  ALA A 168       3.853  12.043  -3.502  1.00  0.00           C  
+ATOM    674  H   ALA A 168       3.465   9.753  -2.350  1.00  0.00           H  
+ATOM    675  HA  ALA A 168       5.643  11.670  -2.423  1.00  0.00           H  
+ATOM    676  HB1 ALA A 168       4.507  11.966  -4.358  1.00  0.00           H  
+ATOM    677  HB2 ALA A 168       3.563  13.074  -3.362  1.00  0.00           H  
+ATOM    678  HB3 ALA A 168       2.972  11.440  -3.666  1.00  0.00           H  
+ATOM    679  N   LYS A 169       3.171  11.883  -0.315  1.00  0.00           N  
+ATOM    680  CA  LYS A 169       2.683  12.572   0.873  1.00  0.00           C  
+ATOM    681  C   LYS A 169       3.773  12.665   1.936  1.00  0.00           C  
+ATOM    682  O   LYS A 169       3.847  13.643   2.679  1.00  0.00           O  
+ATOM    683  CB  LYS A 169       1.460  11.847   1.442  1.00  0.00           C  
+ATOM    684  CG  LYS A 169       0.141  12.338   0.869  1.00  0.00           C  
+ATOM    685  CD  LYS A 169      -0.553  13.308   1.813  1.00  0.00           C  
+ATOM    686  CE  LYS A 169      -1.186  14.467   1.060  1.00  0.00           C  
+ATOM    687  NZ  LYS A 169      -0.505  15.758   1.352  1.00  0.00           N  
+ATOM    688  H   LYS A 169       2.749  11.040  -0.585  1.00  0.00           H  
+ATOM    689  HA  LYS A 169       2.395  13.570   0.582  1.00  0.00           H  
+ATOM    690  HB2 LYS A 169       1.551  10.792   1.229  1.00  0.00           H  
+ATOM    691  HB3 LYS A 169       1.439  11.989   2.513  1.00  0.00           H  
+ATOM    692  HG2 LYS A 169       0.332  12.839  -0.069  1.00  0.00           H  
+ATOM    693  HG3 LYS A 169      -0.504  11.489   0.700  1.00  0.00           H  
+ATOM    694  HD2 LYS A 169      -1.324  12.779   2.354  1.00  0.00           H  
+ATOM    695  HD3 LYS A 169       0.175  13.697   2.511  1.00  0.00           H  
+ATOM    696  HE2 LYS A 169      -1.125  14.270   0.000  1.00  0.00           H  
+ATOM    697  HE3 LYS A 169      -2.223  14.543   1.351  1.00  0.00           H  
+ATOM    698  HZ1 LYS A 169      -0.203  15.786   2.347  1.00  0.00           H  
+ATOM    699  HZ2 LYS A 169       0.331  15.866   0.743  1.00  0.00           H  
+ATOM    700  HZ3 LYS A 169      -1.153  16.552   1.176  1.00  0.00           H  
+ATOM    701  N   ALA A 170       4.617  11.641   2.002  1.00  0.00           N  
+ATOM    702  CA  ALA A 170       5.702  11.607   2.976  1.00  0.00           C  
+ATOM    703  C   ALA A 170       6.963  10.997   2.371  1.00  0.00           C  
+ATOM    704  O   ALA A 170       8.005  10.994   3.059  1.00  0.00           O  
+ATOM    705  CB  ALA A 170       5.278  10.829   4.212  1.00  0.00           C  
+ATOM    706  OXT ALA A 170       6.897  10.529   1.215  1.00  0.00           O  
+ATOM    707  H   ALA A 170       4.506  10.889   1.383  1.00  0.00           H  
+ATOM    708  HA  ALA A 170       5.914  12.624   3.273  1.00  0.00           H  
+ATOM    709  HB1 ALA A 170       5.121   9.793   3.950  1.00  0.00           H  
+ATOM    710  HB2 ALA A 170       4.362  11.246   4.602  1.00  0.00           H  
+ATOM    711  HB3 ALA A 170       6.052  10.896   4.962  1.00  0.00           H                                                  
+ENDMDL   
+MASTER      151    0    0    3    0    0    0    6  352    1    0    4          
+END  

entangled-tps/data/bbl/path.gro

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+size 80334621

entangled-tps/data/bbl/tica_model.pkl

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+oid sha256:00450a5f91daa1948be66c9734cfcbbe8b47adef4da81a67f94ad649bd409c82
+size 2176049

entangled-tps/data/bbl/unfolded.pdb

@@ -0,0 +1,716 @@
+TITLE     MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter
+CRYST1   56.912   56.912   56.912  90.00  90.00  90.00 P 1           1
+MODEL        1
+ATOM      1  N   GLY A 124     -15.235 -28.566 -26.194  1.00  0.00      A    N  
+ATOM      2  CA  GLY A 124     -13.943 -28.304 -25.502  1.00  0.00      A    C  
+ATOM      3  C   GLY A 124     -13.998 -28.701 -24.010  1.00  0.00      A    C  
+ATOM      4  O   GLY A 124     -15.021 -29.042 -23.491  1.00  0.00      A    O  
+ATOM      5  H1  GLY A 124     -15.625 -29.495 -25.939  1.00  0.00      A    H  
+ATOM      6  H2  GLY A 124     -15.935 -27.889 -25.826  1.00  0.00      A    H  
+ATOM      7  H3  GLY A 124     -15.068 -28.460 -27.215  1.00  0.00      A    H  
+ATOM      8  HA2 GLY A 124     -13.511 -27.337 -25.714  1.00  0.00      A    H  
+ATOM      9  HA3 GLY A 124     -13.430 -29.181 -25.868  1.00  0.00      A    H  
+ATOM     10  N   SER A 125     -12.886 -28.580 -23.288  1.00  0.00      A    N  
+ATOM     11  CA  SER A 125     -12.653 -29.147 -21.978  1.00  0.00      A    C  
+ATOM     12  C   SER A 125     -13.603 -28.655 -20.817  1.00  0.00      A    C  
+ATOM     13  O   SER A 125     -13.560 -27.492 -20.398  1.00  0.00      A    O  
+ATOM     14  CB  SER A 125     -11.225 -29.017 -21.520  1.00  0.00      A    C  
+ATOM     15  OG  SER A 125     -10.316 -29.600 -22.435  1.00  0.00      A    O  
+ATOM     16  H   SER A 125     -12.021 -28.337 -23.719  1.00  0.00      A    H  
+ATOM     17  HA  SER A 125     -12.729 -30.223 -22.020  1.00  0.00      A    H  
+ATOM     18  HB2 SER A 125     -10.894 -27.960 -21.439  1.00  0.00      A    H  
+ATOM     19  HB3 SER A 125     -11.010 -29.421 -20.507  1.00  0.00      A    H  
+ATOM     20  HG  SER A 125     -10.280 -30.530 -22.198  1.00  0.00      A    H  
+ATOM     21  N   GLN A 126     -14.556 -29.542 -20.279  1.00  0.00      A    N  
+ATOM     22  CA  GLN A 126     -15.534 -29.221 -19.245  1.00  0.00      A    C  
+ATOM     23  C   GLN A 126     -14.921 -28.626 -18.007  1.00  0.00      A    C  
+ATOM     24  O   GLN A 126     -14.025 -29.248 -17.397  1.00  0.00      A    O  
+ATOM     25  CB  GLN A 126     -16.514 -30.366 -18.880  1.00  0.00      A    C  
+ATOM     26  CG  GLN A 126     -16.021 -31.662 -18.171  1.00  0.00      A    C  
+ATOM     27  CD  GLN A 126     -17.227 -32.713 -18.089  1.00  0.00      A    C  
+ATOM     28  OE1 GLN A 126     -17.254 -33.815 -18.695  1.00  0.00      A    O  
+ATOM     29  NE2 GLN A 126     -18.264 -32.257 -17.382  1.00  0.00      A    N  
+ATOM     30  H   GLN A 126     -14.445 -30.434 -20.710  1.00  0.00      A    H  
+ATOM     31  HA  GLN A 126     -16.098 -28.438 -19.730  1.00  0.00      A    H  
+ATOM     32  HB2 GLN A 126     -17.214 -29.970 -18.113  1.00  0.00      A    H  
+ATOM     33  HB3 GLN A 126     -16.951 -30.722 -19.838  1.00  0.00      A    H  
+ATOM     34  HG2 GLN A 126     -15.190 -32.172 -18.703  1.00  0.00      A    H  
+ATOM     35  HG3 GLN A 126     -15.714 -31.437 -17.127  1.00  0.00      A    H  
+ATOM     36 HE21 GLN A 126     -19.102 -32.803 -17.387  1.00  0.00      A    H  
+ATOM     37 HE22 GLN A 126     -18.203 -31.484 -16.751  1.00  0.00      A    H  
+ATOM     38  N   ASN A 127     -15.316 -27.415 -17.503  1.00  0.00      A    N  
+ATOM     39  CA  ASN A 127     -14.843 -26.726 -16.300  1.00  0.00      A    C  
+ATOM     40  C   ASN A 127     -13.367 -26.099 -16.420  1.00  0.00      A    C  
+ATOM     41  O   ASN A 127     -12.615 -26.015 -15.436  1.00  0.00      A    O  
+ATOM     42  CB  ASN A 127     -15.051 -27.584 -14.950  1.00  0.00      A    C  
+ATOM     43  CG  ASN A 127     -16.431 -28.258 -14.808  1.00  0.00      A    C  
+ATOM     44  OD1 ASN A 127     -17.492 -27.627 -14.728  1.00  0.00      A    O  
+ATOM     45  ND2 ASN A 127     -16.356 -29.593 -14.678  1.00  0.00      A    N  
+ATOM     46  H   ASN A 127     -16.043 -27.060 -18.086  1.00  0.00      A    H  
+ATOM     47  HA  ASN A 127     -15.528 -25.897 -16.201  1.00  0.00      A    H  
+ATOM     48  HB2 ASN A 127     -14.254 -28.354 -14.875  1.00  0.00      A    H  
+ATOM     49  HB3 ASN A 127     -14.997 -26.793 -14.172  1.00  0.00      A    H  
+ATOM     50 HD21 ASN A 127     -17.269 -29.994 -14.757  1.00  0.00      A    H  
+ATOM     51 HD22 ASN A 127     -15.505 -29.985 -14.330  1.00  0.00      A    H  
+ATOM     52  N   ASN A 128     -12.882 -25.775 -17.671  1.00  0.00      A    N  
+ATOM     53  CA  ASN A 128     -11.620 -25.129 -17.944  1.00  0.00      A    C  
+ATOM     54  C   ASN A 128     -11.889 -23.723 -18.587  1.00  0.00      A    C  
+ATOM     55  O   ASN A 128     -12.708 -23.630 -19.473  1.00  0.00      A    O  
+ATOM     56  CB  ASN A 128     -10.688 -25.954 -18.851  1.00  0.00      A    C  
+ATOM     57  CG  ASN A 128     -10.427 -27.283 -18.264  1.00  0.00      A    C  
+ATOM     58  OD1 ASN A 128     -11.268 -28.080 -17.884  1.00  0.00      A    O  
+ATOM     59  ND2 ASN A 128      -9.092 -27.677 -18.185  1.00  0.00      A    N  
+ATOM     60  H   ASN A 128     -13.391 -25.964 -18.507  1.00  0.00      A    H  
+ATOM     61  HA  ASN A 128     -11.070 -24.986 -17.025  1.00  0.00      A    H  
+ATOM     62  HB2 ASN A 128     -11.158 -26.111 -19.845  1.00  0.00      A    H  
+ATOM     63  HB3 ASN A 128      -9.780 -25.334 -19.009  1.00  0.00      A    H  
+ATOM     64 HD21 ASN A 128      -8.904 -28.573 -17.781  1.00  0.00      A    H  
+ATOM     65 HD22 ASN A 128      -8.359 -27.103 -18.551  1.00  0.00      A    H  
+ATOM     66  N   ASP A 129     -11.058 -22.743 -18.154  1.00  0.00      A    N  
+ATOM     67  CA  ASP A 129     -11.197 -21.300 -18.534  1.00  0.00      A    C  
+ATOM     68  C   ASP A 129     -10.194 -20.841 -19.579  1.00  0.00      A    C  
+ATOM     69  O   ASP A 129      -9.137 -21.426 -19.688  1.00  0.00      A    O  
+ATOM     70  CB  ASP A 129     -10.924 -20.374 -17.318  1.00  0.00      A    C  
+ATOM     71  CG  ASP A 129     -12.218 -20.265 -16.519  1.00  0.00      A    C  
+ATOM     72  OD1 ASP A 129     -13.316 -19.980 -17.128  1.00  0.00      A    O  
+ATOM     73  OD2 ASP A 129     -12.102 -20.325 -15.270  1.00  0.00      A    O  
+ATOM     74  H   ASP A 129     -10.310 -22.962 -17.532  1.00  0.00      A    H  
+ATOM     75  HA  ASP A 129     -12.165 -21.050 -18.942  1.00  0.00      A    H  
+ATOM     76  HB2 ASP A 129     -10.033 -20.772 -16.788  1.00  0.00      A    H  
+ATOM     77  HB3 ASP A 129     -10.683 -19.360 -17.702  1.00  0.00      A    H  
+ATOM     78  N   ALA A 130     -10.476 -19.809 -20.349  1.00  0.00      A    N  
+ATOM     79  CA  ALA A 130      -9.608 -19.449 -21.443  1.00  0.00      A    C  
+ATOM     80  C   ALA A 130      -8.481 -18.469 -21.057  1.00  0.00      A    C  
+ATOM     81  O   ALA A 130      -8.798 -17.437 -20.429  1.00  0.00      A    O  
+ATOM     82  CB  ALA A 130     -10.471 -18.890 -22.525  1.00  0.00      A    C  
+ATOM     83  H   ALA A 130     -11.231 -19.228 -20.057  1.00  0.00      A    H  
+ATOM     84  HA  ALA A 130      -9.212 -20.394 -21.783  1.00  0.00      A    H  
+ATOM     85  HB1 ALA A 130     -10.600 -17.787 -22.513  1.00  0.00      A    H  
+ATOM     86  HB2 ALA A 130     -11.448 -19.419 -22.530  1.00  0.00      A    H  
+ATOM     87  HB3 ALA A 130     -10.014 -18.997 -23.533  1.00  0.00      A    H  
+ATOM     88  N   LEU A 131      -7.210 -18.767 -21.391  1.00  0.00      A    N  
+ATOM     89  CA  LEU A 131      -6.199 -17.681 -21.161  1.00  0.00      A    C  
+ATOM     90  C   LEU A 131      -6.270 -16.632 -22.214  1.00  0.00      A    C  
+ATOM     91  O   LEU A 131      -6.319 -16.918 -23.412  1.00  0.00      A    O  
+ATOM     92  CB  LEU A 131      -4.707 -18.270 -21.230  1.00  0.00      A    C  
+ATOM     93  CG  LEU A 131      -3.567 -17.373 -20.736  1.00  0.00      A    C  
+ATOM     94  CD1 LEU A 131      -3.657 -17.095 -19.239  1.00  0.00      A    C  
+ATOM     95  CD2 LEU A 131      -2.198 -18.097 -20.825  1.00  0.00      A    C  
+ATOM     96  H   LEU A 131      -6.891 -19.645 -21.740  1.00  0.00      A    H  
+ATOM     97  HA  LEU A 131      -6.325 -17.178 -20.213  1.00  0.00      A    H  
+ATOM     98  HB2 LEU A 131      -4.661 -19.154 -20.559  1.00  0.00      A    H  
+ATOM     99  HB3 LEU A 131      -4.491 -18.543 -22.285  1.00  0.00      A    H  
+ATOM    100  HG  LEU A 131      -3.503 -16.468 -21.377  1.00  0.00      A    H  
+ATOM    101 HD11 LEU A 131      -3.603 -17.942 -18.522  1.00  0.00      A    H  
+ATOM    102 HD12 LEU A 131      -2.775 -16.474 -18.976  1.00  0.00      A    H  
+ATOM    103 HD13 LEU A 131      -4.552 -16.443 -19.154  1.00  0.00      A    H  
+ATOM    104 HD21 LEU A 131      -1.983 -18.064 -21.915  1.00  0.00      A    H  
+ATOM    105 HD22 LEU A 131      -1.397 -17.486 -20.358  1.00  0.00      A    H  
+ATOM    106 HD23 LEU A 131      -2.129 -19.116 -20.386  1.00  0.00      A    H  
+ATOM    107  N   SER A 132      -6.297 -15.374 -21.789  1.00  0.00      A    N  
+ATOM    108  CA  SER A 132      -6.632 -14.251 -22.625  1.00  0.00      A    C  
+ATOM    109  C   SER A 132      -5.369 -13.469 -22.601  1.00  0.00      A    C  
+ATOM    110  O   SER A 132      -4.988 -12.903 -21.586  1.00  0.00      A    O  
+ATOM    111  CB  SER A 132      -7.799 -13.372 -22.056  1.00  0.00      A    C  
+ATOM    112  OG  SER A 132      -8.106 -12.217 -22.848  1.00  0.00      A    O  
+ATOM    113  H   SER A 132      -6.363 -15.334 -20.795  1.00  0.00      A    H  
+ATOM    114  HA  SER A 132      -6.937 -14.705 -23.556  1.00  0.00      A    H  
+ATOM    115  HB2 SER A 132      -8.723 -13.968 -21.897  1.00  0.00      A    H  
+ATOM    116  HB3 SER A 132      -7.423 -13.011 -21.075  1.00  0.00      A    H  
+ATOM    117  HG  SER A 132      -8.953 -11.856 -22.575  1.00  0.00      A    H  
+ATOM    118  N   PRO A 133      -4.700 -13.406 -23.703  1.00  0.00      A    N  
+ATOM    119  CA  PRO A 133      -3.415 -12.657 -23.819  1.00  0.00      A    C  
+ATOM    120  C   PRO A 133      -3.480 -11.208 -23.401  1.00  0.00      A    C  
+ATOM    121  O   PRO A 133      -2.476 -10.638 -22.926  1.00  0.00      A    O  
+ATOM    122  CB  PRO A 133      -2.974 -12.770 -25.286  1.00  0.00      A    C  
+ATOM    123  CG  PRO A 133      -3.774 -13.919 -25.879  1.00  0.00      A    C  
+ATOM    124  CD  PRO A 133      -5.033 -13.982 -24.989  1.00  0.00      A    C  
+ATOM    125  HA  PRO A 133      -2.741 -13.157 -23.140  1.00  0.00      A    H  
+ATOM    126  HB2 PRO A 133      -3.272 -11.852 -25.836  1.00  0.00      A    H  
+ATOM    127  HB3 PRO A 133      -1.865 -12.824 -25.302  1.00  0.00      A    H  
+ATOM    128  HG2 PRO A 133      -3.996 -13.773 -26.957  1.00  0.00      A    H  
+ATOM    129  HG3 PRO A 133      -3.209 -14.867 -25.752  1.00  0.00      A    H  
+ATOM    130  HD2 PRO A 133      -5.781 -13.388 -25.557  1.00  0.00      A    H  
+ATOM    131  HD3 PRO A 133      -5.421 -15.001 -24.777  1.00  0.00      A    H  
+ATOM    132  N   ALA A 134      -4.646 -10.483 -23.671  1.00  0.00      A    N  
+ATOM    133  CA  ALA A 134      -4.733  -9.126 -23.152  1.00  0.00      A    C  
+ATOM    134  C   ALA A 134      -4.919  -8.940 -21.646  1.00  0.00      A    C  
+ATOM    135  O   ALA A 134      -4.464  -7.942 -21.039  1.00  0.00      A    O  
+ATOM    136  CB  ALA A 134      -5.935  -8.465 -23.873  1.00  0.00      A    C  
+ATOM    137  H   ALA A 134      -5.363 -10.947 -24.186  1.00  0.00      A    H  
+ATOM    138  HA  ALA A 134      -3.891  -8.503 -23.416  1.00  0.00      A    H  
+ATOM    139  HB1 ALA A 134      -6.803  -9.072 -23.537  1.00  0.00      A    H  
+ATOM    140  HB2 ALA A 134      -5.769  -8.556 -24.968  1.00  0.00      A    H  
+ATOM    141  HB3 ALA A 134      -6.057  -7.376 -23.695  1.00  0.00      A    H  
+ATOM    142  N   ILE A 135      -5.548  -9.921 -20.885  1.00  0.00      A    N  
+ATOM    143  CA  ILE A 135      -5.667  -9.849 -19.469  1.00  0.00      A    C  
+ATOM    144  C   ILE A 135      -4.321 -10.395 -18.843  1.00  0.00      A    C  
+ATOM    145  O   ILE A 135      -3.737  -9.702 -18.034  1.00  0.00      A    O  
+ATOM    146  CB  ILE A 135      -6.845 -10.542 -18.772  1.00  0.00      A    C  
+ATOM    147  CG1 ILE A 135      -8.157 -10.119 -19.465  1.00  0.00      A    C  
+ATOM    148  CG2 ILE A 135      -6.871 -10.065 -17.308  1.00  0.00      A    C  
+ATOM    149  CD1 ILE A 135      -8.482  -8.565 -19.345  1.00  0.00      A    C  
+ATOM    150  H   ILE A 135      -5.947 -10.732 -21.305  1.00  0.00      A    H  
+ATOM    151  HA  ILE A 135      -5.745  -8.810 -19.186  1.00  0.00      A    H  
+ATOM    152  HB  ILE A 135      -6.844 -11.653 -18.774  1.00  0.00      A    H  
+ATOM    153 HG12 ILE A 135      -8.053 -10.530 -20.492  1.00  0.00      A    H  
+ATOM    154 HG13 ILE A 135      -9.023 -10.708 -19.094  1.00  0.00      A    H  
+ATOM    155 HG21 ILE A 135      -7.789 -10.429 -16.800  1.00  0.00      A    H  
+ATOM    156 HG22 ILE A 135      -6.026 -10.513 -16.742  1.00  0.00      A    H  
+ATOM    157 HG23 ILE A 135      -6.950  -8.957 -17.267  1.00  0.00      A    H  
+ATOM    158 HD11 ILE A 135      -9.492  -8.404 -19.780  1.00  0.00      A    H  
+ATOM    159 HD12 ILE A 135      -8.472  -8.281 -18.271  1.00  0.00      A    H  
+ATOM    160 HD13 ILE A 135      -7.757  -8.023 -19.989  1.00  0.00      A    H  
+ATOM    161  N   ARG A 136      -3.780 -11.437 -19.439  1.00  0.00      A    N  
+ATOM    162  CA  ARG A 136      -2.470 -11.949 -19.094  1.00  0.00      A    C  
+ATOM    163  C   ARG A 136      -1.279 -11.042 -19.268  1.00  0.00      A    C  
+ATOM    164  O   ARG A 136      -0.399 -10.966 -18.421  1.00  0.00      A    O  
+ATOM    165  CB  ARG A 136      -2.113 -13.179 -19.973  1.00  0.00      A    C  
+ATOM    166  CG  ARG A 136      -0.735 -13.809 -19.820  1.00  0.00      A    C  
+ATOM    167  CD  ARG A 136      -0.436 -14.327 -18.388  1.00  0.00      A    C  
+ATOM    168  NE  ARG A 136       0.987 -14.833 -18.465  1.00  0.00      A    N  
+ATOM    169  CZ  ARG A 136       1.826 -14.957 -17.451  1.00  0.00      A    C  
+ATOM    170  NH1 ARG A 136       1.406 -14.824 -16.229  1.00  0.00      A    N  
+ATOM    171  NH2 ARG A 136       3.049 -15.500 -17.692  1.00  0.00      A    N  
+ATOM    172  H   ARG A 136      -4.335 -12.001 -20.046  1.00  0.00      A    H  
+ATOM    173  HA  ARG A 136      -2.458 -12.323 -18.080  1.00  0.00      A    H  
+ATOM    174  HB2 ARG A 136      -2.923 -13.939 -19.936  1.00  0.00      A    H  
+ATOM    175  HB3 ARG A 136      -2.132 -12.816 -21.023  1.00  0.00      A    H  
+ATOM    176  HG2 ARG A 136      -0.499 -14.604 -20.560  1.00  0.00      A    H  
+ATOM    177  HG3 ARG A 136       0.036 -13.031 -20.000  1.00  0.00      A    H  
+ATOM    178  HD2 ARG A 136      -0.402 -13.514 -17.631  1.00  0.00      A    H  
+ATOM    179  HD3 ARG A 136      -1.154 -15.119 -18.085  1.00  0.00      A    H  
+ATOM    180  HE  ARG A 136       1.332 -15.082 -19.370  1.00  0.00      A    H  
+ATOM    181 HH11 ARG A 136       2.015 -15.050 -15.469  1.00  0.00      A    H  
+ATOM    182 HH12 ARG A 136       0.560 -14.390 -15.921  1.00  0.00      A    H  
+ATOM    183 HH21 ARG A 136       3.305 -15.741 -18.628  1.00  0.00      A    H  
+ATOM    184 HH22 ARG A 136       3.672 -15.688 -16.932  1.00  0.00      A    H  
+ATOM    185  N   ARG A 137      -1.154 -10.289 -20.390  1.00  0.00      A    N  
+ATOM    186  CA  ARG A 137      -0.144  -9.232 -20.518  1.00  0.00      A    C  
+ATOM    187  C   ARG A 137      -0.336  -7.992 -19.681  1.00  0.00      A    C  
+ATOM    188  O   ARG A 137       0.677  -7.451 -19.179  1.00  0.00      A    O  
+ATOM    189  CB  ARG A 137      -0.014  -8.755 -22.015  1.00  0.00      A    C  
+ATOM    190  CG  ARG A 137       1.168  -7.847 -22.352  1.00  0.00      A    C  
+ATOM    191  CD  ARG A 137       1.510  -7.639 -23.840  1.00  0.00      A    C  
+ATOM    192  NE  ARG A 137       2.985  -7.234 -23.944  1.00  0.00      A    N  
+ATOM    193  CZ  ARG A 137       3.691  -7.337 -25.051  1.00  0.00      A    C  
+ATOM    194  NH1 ARG A 137       3.015  -7.812 -26.139  1.00  0.00      A    N  
+ATOM    195  NH2 ARG A 137       4.954  -7.047 -25.098  1.00  0.00      A    N  
+ATOM    196  H   ARG A 137      -1.782 -10.327 -21.162  1.00  0.00      A    H  
+ATOM    197  HA  ARG A 137       0.815  -9.628 -20.219  1.00  0.00      A    H  
+ATOM    198  HB2 ARG A 137       0.093  -9.702 -22.586  1.00  0.00      A    H  
+ATOM    199  HB3 ARG A 137      -0.986  -8.274 -22.255  1.00  0.00      A    H  
+ATOM    200  HG2 ARG A 137       1.215  -6.826 -21.917  1.00  0.00      A    H  
+ATOM    201  HG3 ARG A 137       2.061  -8.245 -21.824  1.00  0.00      A    H  
+ATOM    202  HD2 ARG A 137       1.322  -8.603 -24.357  1.00  0.00      A    H  
+ATOM    203  HD3 ARG A 137       0.828  -6.861 -24.245  1.00  0.00      A    H  
+ATOM    204  HE  ARG A 137       3.428  -6.752 -23.187  1.00  0.00      A    H  
+ATOM    205 HH11 ARG A 137       3.553  -8.108 -26.929  1.00  0.00      A    H  
+ATOM    206 HH12 ARG A 137       2.017  -7.851 -26.104  1.00  0.00      A    H  
+ATOM    207 HH21 ARG A 137       5.424  -6.770 -24.260  1.00  0.00      A    H  
+ATOM    208 HH22 ARG A 137       5.531  -7.019 -25.915  1.00  0.00      A    H  
+ATOM    209  N   LEU A 138      -1.596  -7.509 -19.415  1.00  0.00      A    N  
+ATOM    210  CA  LEU A 138      -1.697  -6.391 -18.475  1.00  0.00      A    C  
+ATOM    211  C   LEU A 138      -1.405  -6.774 -17.010  1.00  0.00      A    C  
+ATOM    212  O   LEU A 138      -0.902  -5.967 -16.194  1.00  0.00      A    O  
+ATOM    213  CB  LEU A 138      -3.081  -5.669 -18.612  1.00  0.00      A    C  
+ATOM    214  CG  LEU A 138      -4.477  -6.249 -18.054  1.00  0.00      A    C  
+ATOM    215  CD1 LEU A 138      -4.706  -5.968 -16.541  1.00  0.00      A    C  
+ATOM    216  CD2 LEU A 138      -5.700  -5.845 -18.901  1.00  0.00      A    C  
+ATOM    217  H   LEU A 138      -2.427  -7.890 -19.812  1.00  0.00      A    H  
+ATOM    218  HA  LEU A 138      -0.908  -5.674 -18.647  1.00  0.00      A    H  
+ATOM    219  HB2 LEU A 138      -3.001  -4.608 -18.295  1.00  0.00      A    H  
+ATOM    220  HB3 LEU A 138      -3.207  -5.640 -19.715  1.00  0.00      A    H  
+ATOM    221  HG  LEU A 138      -4.539  -7.338 -18.265  1.00  0.00      A    H  
+ATOM    222 HD11 LEU A 138      -3.934  -6.495 -15.941  1.00  0.00      A    H  
+ATOM    223 HD12 LEU A 138      -4.482  -4.923 -16.238  1.00  0.00      A    H  
+ATOM    224 HD13 LEU A 138      -5.697  -6.164 -16.077  1.00  0.00      A    H  
+ATOM    225 HD21 LEU A 138      -5.959  -4.771 -18.779  1.00  0.00      A    H  
+ATOM    226 HD22 LEU A 138      -5.618  -6.027 -19.994  1.00  0.00      A    H  
+ATOM    227 HD23 LEU A 138      -6.551  -6.458 -18.536  1.00  0.00      A    H  
+ATOM    228  N   LEU A 139      -1.589  -8.073 -16.650  1.00  0.00      A    N  
+ATOM    229  CA  LEU A 139      -1.085  -8.589 -15.374  1.00  0.00      A    C  
+ATOM    230  C   LEU A 139       0.480  -8.645 -15.289  1.00  0.00      A    C  
+ATOM    231  O   LEU A 139       1.072  -8.008 -14.387  1.00  0.00      A    O  
+ATOM    232  CB  LEU A 139      -1.676  -9.917 -15.060  1.00  0.00      A    C  
+ATOM    233  CG  LEU A 139      -3.186  -9.884 -14.779  1.00  0.00      A    C  
+ATOM    234  CD1 LEU A 139      -3.643 -11.319 -14.766  1.00  0.00      A    C  
+ATOM    235  CD2 LEU A 139      -3.461  -9.190 -13.425  1.00  0.00      A    C  
+ATOM    236  H   LEU A 139      -1.946  -8.809 -17.220  1.00  0.00      A    H  
+ATOM    237  HA  LEU A 139      -1.411  -7.991 -14.536  1.00  0.00      A    H  
+ATOM    238  HB2 LEU A 139      -1.454 -10.587 -15.918  1.00  0.00      A    H  
+ATOM    239  HB3 LEU A 139      -1.130 -10.428 -14.238  1.00  0.00      A    H  
+ATOM    240  HG  LEU A 139      -3.812  -9.428 -15.576  1.00  0.00      A    H  
+ATOM    241 HD11 LEU A 139      -4.641 -11.362 -14.280  1.00  0.00      A    H  
+ATOM    242 HD12 LEU A 139      -3.592 -11.721 -15.801  1.00  0.00      A    H  
+ATOM    243 HD13 LEU A 139      -2.967 -11.932 -14.132  1.00  0.00      A    H  
+ATOM    244 HD21 LEU A 139      -3.101  -8.139 -13.415  1.00  0.00      A    H  
+ATOM    245 HD22 LEU A 139      -4.564  -9.214 -13.293  1.00  0.00      A    H  
+ATOM    246 HD23 LEU A 139      -3.038  -9.785 -12.587  1.00  0.00      A    H  
+ATOM    247  N   ALA A 140       1.052  -9.434 -16.235  1.00  0.00      A    N  
+ATOM    248  CA  ALA A 140       2.444  -9.834 -16.348  1.00  0.00      A    C  
+ATOM    249  C   ALA A 140       3.021  -9.564 -17.817  1.00  0.00      A    C  
+ATOM    250  O   ALA A 140       2.895 -10.339 -18.744  1.00  0.00      A    O  
+ATOM    251  CB  ALA A 140       2.575 -11.365 -16.014  1.00  0.00      A    C  
+ATOM    252  H   ALA A 140       0.523  -9.990 -16.872  1.00  0.00      A    H  
+ATOM    253  HA  ALA A 140       3.076  -9.207 -15.736  1.00  0.00      A    H  
+ATOM    254  HB1 ALA A 140       3.618 -11.742 -15.948  1.00  0.00      A    H  
+ATOM    255  HB2 ALA A 140       1.982 -11.944 -16.754  1.00  0.00      A    H  
+ATOM    256  HB3 ALA A 140       2.131 -11.614 -15.027  1.00  0.00      A    H  
+ATOM    257  N   GLU A 141       3.587  -8.391 -18.032  1.00  0.00      A    N  
+ATOM    258  CA  GLU A 141       4.167  -8.016 -19.348  1.00  0.00      A    C  
+ATOM    259  C   GLU A 141       5.320  -8.949 -19.801  1.00  0.00      A    C  
+ATOM    260  O   GLU A 141       6.211  -9.336 -19.025  1.00  0.00      A    O  
+ATOM    261  CB  GLU A 141       4.452  -6.533 -19.200  1.00  0.00      A    C  
+ATOM    262  CG  GLU A 141       5.380  -5.899 -20.251  1.00  0.00      A    C  
+ATOM    263  CD  GLU A 141       4.823  -5.899 -21.706  1.00  0.00      A    C  
+ATOM    264  OE1 GLU A 141       5.387  -6.691 -22.533  1.00  0.00      A    O  
+ATOM    265  OE2 GLU A 141       3.836  -5.137 -22.006  1.00  0.00      A    O  
+ATOM    266  H   GLU A 141       3.552  -7.666 -17.350  1.00  0.00      A    H  
+ATOM    267  HA  GLU A 141       3.347  -8.186 -20.030  1.00  0.00      A    H  
+ATOM    268  HB2 GLU A 141       3.508  -5.948 -19.178  1.00  0.00      A    H  
+ATOM    269  HB3 GLU A 141       4.867  -6.278 -18.201  1.00  0.00      A    H  
+ATOM    270  HG2 GLU A 141       5.640  -4.831 -20.091  1.00  0.00      A    H  
+ATOM    271  HG3 GLU A 141       6.413  -6.306 -20.209  1.00  0.00      A    H  
+ATOM    272  N   TRP A 142       5.280  -9.371 -21.076  1.00  0.00      A    N  
+ATOM    273  CA  TRP A 142       6.227 -10.289 -21.789  1.00  0.00      A    C  
+ATOM    274  C   TRP A 142       7.612  -9.724 -21.904  1.00  0.00      A    C  
+ATOM    275  O   TRP A 142       8.545 -10.455 -21.855  1.00  0.00      A    O  
+ATOM    276  CB  TRP A 142       5.697 -10.785 -23.146  1.00  0.00      A    C  
+ATOM    277  CG  TRP A 142       4.264 -11.380 -22.960  1.00  0.00      A    C  
+ATOM    278  CD1 TRP A 142       3.588 -11.758 -21.815  1.00  0.00      A    C  
+ATOM    279  CD2 TRP A 142       3.299 -11.376 -24.069  1.00  0.00      A    C  
+ATOM    280  NE1 TRP A 142       2.237 -11.889 -22.163  1.00  0.00      A    N  
+ATOM    281  CE2 TRP A 142       2.024 -11.723 -23.480  1.00  0.00      A    C  
+ATOM    282  CE3 TRP A 142       3.391 -11.042 -25.392  1.00  0.00      A    C  
+ATOM    283  CZ2 TRP A 142       0.851 -11.736 -24.261  1.00  0.00      A    C  
+ATOM    284  CZ3 TRP A 142       2.231 -11.051 -26.190  1.00  0.00      A    C  
+ATOM    285  CH2 TRP A 142       0.987 -11.376 -25.563  1.00  0.00      A    C  
+ATOM    286  H   TRP A 142       4.529  -8.992 -21.611  1.00  0.00      A    H  
+ATOM    287  HA  TRP A 142       6.381 -11.046 -21.034  1.00  0.00      A    H  
+ATOM    288  HB2 TRP A 142       5.792 -10.119 -24.031  1.00  0.00      A    H  
+ATOM    289  HB3 TRP A 142       6.330 -11.633 -23.485  1.00  0.00      A    H  
+ATOM    290  HD1 TRP A 142       3.955 -11.848 -20.803  1.00  0.00      A    H  
+ATOM    291  HE1 TRP A 142       1.537 -12.058 -21.505  1.00  0.00      A    H  
+ATOM    292  HE3 TRP A 142       4.358 -10.873 -25.841  1.00  0.00      A    H  
+ATOM    293  HZ2 TRP A 142      -0.126 -11.944 -23.850  1.00  0.00      A    H  
+ATOM    294  HZ3 TRP A 142       2.270 -10.971 -27.266  1.00  0.00      A    H  
+ATOM    295  HH2 TRP A 142       0.130 -11.164 -26.185  1.00  0.00      A    H  
+ATOM    296  N   ASN A 143       7.685  -8.409 -22.068  1.00  0.00      A    N  
+ATOM    297  CA  ASN A 143       8.978  -7.746 -22.219  1.00  0.00      A    C  
+ATOM    298  C   ASN A 143       9.239  -6.701 -21.198  1.00  0.00      A    C  
+ATOM    299  O   ASN A 143       8.679  -5.615 -21.253  1.00  0.00      A    O  
+ATOM    300  CB  ASN A 143       8.994  -7.100 -23.631  1.00  0.00      A    C  
+ATOM    301  CG  ASN A 143       8.711  -8.106 -24.763  1.00  0.00      A    C  
+ATOM    302  OD1 ASN A 143       7.616  -8.063 -25.379  1.00  0.00      A    O  
+ATOM    303  ND2 ASN A 143       9.679  -8.997 -24.960  1.00  0.00      A    N  
+ATOM    304  H   ASN A 143       6.864  -7.849 -22.150  1.00  0.00      A    H  
+ATOM    305  HA  ASN A 143       9.795  -8.441 -22.092  1.00  0.00      A    H  
+ATOM    306  HB2 ASN A 143       8.323  -6.216 -23.670  1.00  0.00      A    H  
+ATOM    307  HB3 ASN A 143      10.033  -6.723 -23.736  1.00  0.00      A    H  
+ATOM    308 HD21 ASN A 143      10.486  -8.752 -24.422  1.00  0.00      A    H  
+ATOM    309 HD22 ASN A 143       9.535  -9.644 -25.709  1.00  0.00      A    H  
+ATOM    310  N   LEU A 144       9.977  -6.982 -20.038  1.00  0.00      A    N  
+ATOM    311  CA  LEU A 144      10.120  -5.975 -19.013  1.00  0.00      A    C  
+ATOM    312  C   LEU A 144      11.411  -6.447 -18.299  1.00  0.00      A    C  
+ATOM    313  O   LEU A 144      11.483  -7.599 -17.896  1.00  0.00      A    O  
+ATOM    314  CB  LEU A 144       8.951  -5.940 -18.094  1.00  0.00      A    C  
+ATOM    315  CG  LEU A 144       9.039  -4.825 -17.075  1.00  0.00      A    C  
+ATOM    316  CD1 LEU A 144       9.498  -3.473 -17.608  1.00  0.00      A    C  
+ATOM    317  CD2 LEU A 144       7.541  -4.555 -16.660  1.00  0.00      A    C  
+ATOM    318  H   LEU A 144      10.580  -7.774 -19.983  1.00  0.00      A    H  
+ATOM    319  HA  LEU A 144      10.457  -5.053 -19.463  1.00  0.00      A    H  
+ATOM    320  HB2 LEU A 144       7.988  -5.794 -18.628  1.00  0.00      A    H  
+ATOM    321  HB3 LEU A 144       8.874  -6.840 -17.447  1.00  0.00      A    H  
+ATOM    322  HG  LEU A 144       9.630  -5.107 -16.178  1.00  0.00      A    H  
+ATOM    323 HD11 LEU A 144       9.039  -3.317 -18.607  1.00  0.00      A    H  
+ATOM    324 HD12 LEU A 144       9.403  -2.605 -16.921  1.00  0.00      A    H  
+ATOM    325 HD13 LEU A 144      10.580  -3.442 -17.859  1.00  0.00      A    H  
+ATOM    326 HD21 LEU A 144       7.249  -5.479 -16.116  1.00  0.00      A    H  
+ATOM    327 HD22 LEU A 144       7.356  -3.675 -16.007  1.00  0.00      A    H  
+ATOM    328 HD23 LEU A 144       6.967  -4.429 -17.603  1.00  0.00      A    H  
+ATOM    329  N   ASP A 145      12.420  -5.593 -17.981  1.00  0.00      A    N  
+ATOM    330  CA  ASP A 145      13.705  -6.063 -17.555  1.00  0.00      A    C  
+ATOM    331  C   ASP A 145      13.788  -6.040 -16.045  1.00  0.00      A    C  
+ATOM    332  O   ASP A 145      13.048  -5.352 -15.324  1.00  0.00      A    O  
+ATOM    333  CB  ASP A 145      14.805  -5.065 -18.046  1.00  0.00      A    C  
+ATOM    334  CG  ASP A 145      14.848  -5.005 -19.526  1.00  0.00      A    C  
+ATOM    335  OD1 ASP A 145      15.130  -6.016 -20.110  1.00  0.00      A    O  
+ATOM    336  OD2 ASP A 145      14.658  -3.877 -20.095  1.00  0.00      A    O  
+ATOM    337  H   ASP A 145      12.284  -4.608 -18.052  1.00  0.00      A    H  
+ATOM    338  HA  ASP A 145      13.895  -7.064 -17.914  1.00  0.00      A    H  
+ATOM    339  HB2 ASP A 145      14.558  -4.015 -17.784  1.00  0.00      A    H  
+ATOM    340  HB3 ASP A 145      15.812  -5.318 -17.650  1.00  0.00      A    H  
+ATOM    341  N   ALA A 146      14.748  -6.823 -15.473  1.00  0.00      A    N  
+ATOM    342  CA  ALA A 146      15.082  -6.725 -14.110  1.00  0.00      A    C  
+ATOM    343  C   ALA A 146      16.539  -6.396 -13.868  1.00  0.00      A    C  
+ATOM    344  O   ALA A 146      17.472  -6.779 -14.558  1.00  0.00      A    O  
+ATOM    345  CB  ALA A 146      14.721  -8.013 -13.457  1.00  0.00      A    C  
+ATOM    346  H   ALA A 146      15.373  -7.341 -16.052  1.00  0.00      A    H  
+ATOM    347  HA  ALA A 146      14.687  -5.783 -13.758  1.00  0.00      A    H  
+ATOM    348  HB1 ALA A 146      13.673  -8.152 -13.800  1.00  0.00      A    H  
+ATOM    349  HB2 ALA A 146      14.793  -8.070 -12.350  1.00  0.00      A    H  
+ATOM    350  HB3 ALA A 146      15.428  -8.781 -13.839  1.00  0.00      A    H  
+ATOM    351  N   SER A 147      16.810  -5.687 -12.670  1.00  0.00      A    N  
+ATOM    352  CA  SER A 147      18.107  -5.273 -12.339  1.00  0.00      A    C  
+ATOM    353  C   SER A 147      19.057  -6.429 -11.887  1.00  0.00      A    C  
+ATOM    354  O   SER A 147      18.834  -7.190 -10.967  1.00  0.00      A    O  
+ATOM    355  CB  SER A 147      18.065  -4.412 -11.020  1.00  0.00      A    C  
+ATOM    356  OG  SER A 147      17.528  -3.183 -11.173  1.00  0.00      A    O  
+ATOM    357  H   SER A 147      16.153  -5.473 -11.951  1.00  0.00      A    H  
+ATOM    358  HA  SER A 147      18.530  -4.809 -13.217  1.00  0.00      A    H  
+ATOM    359  HB2 SER A 147      17.495  -4.980 -10.254  1.00  0.00      A    H  
+ATOM    360  HB3 SER A 147      19.139  -4.295 -10.760  1.00  0.00      A    H  
+ATOM    361  HG  SER A 147      17.063  -2.948 -10.367  1.00  0.00      A    H  
+ATOM    362  N   ALA A 148      20.128  -6.604 -12.723  1.00  0.00      A    N  
+ATOM    363  CA  ALA A 148      20.966  -7.791 -12.728  1.00  0.00      A    C  
+ATOM    364  C   ALA A 148      21.999  -7.833 -11.556  1.00  0.00      A    C  
+ATOM    365  O   ALA A 148      22.506  -8.861 -11.286  1.00  0.00      A    O  
+ATOM    366  CB  ALA A 148      21.713  -7.830 -14.101  1.00  0.00      A    C  
+ATOM    367  H   ALA A 148      20.309  -5.887 -13.392  1.00  0.00      A    H  
+ATOM    368  HA  ALA A 148      20.328  -8.661 -12.671  1.00  0.00      A    H  
+ATOM    369  HB1 ALA A 148      22.406  -6.971 -14.228  1.00  0.00      A    H  
+ATOM    370  HB2 ALA A 148      20.965  -7.704 -14.914  1.00  0.00      A    H  
+ATOM    371  HB3 ALA A 148      22.241  -8.803 -14.189  1.00  0.00      A    H  
+ATOM    372  N   ILE A 149      22.252  -6.794 -10.749  1.00  0.00      A    N  
+ATOM    373  CA  ILE A 149      23.199  -6.885  -9.636  1.00  0.00      A    C  
+ATOM    374  C   ILE A 149      22.628  -7.391  -8.424  1.00  0.00      A    C  
+ATOM    375  O   ILE A 149      21.457  -7.134  -8.224  1.00  0.00      A    O  
+ATOM    376  CB  ILE A 149      23.832  -5.561  -9.345  1.00  0.00      A    C  
+ATOM    377  CG1 ILE A 149      25.178  -5.524  -8.580  1.00  0.00      A    C  
+ATOM    378  CG2 ILE A 149      22.850  -4.507  -8.665  1.00  0.00      A    C  
+ATOM    379  CD1 ILE A 149      26.350  -6.291  -9.269  1.00  0.00      A    C  
+ATOM    380  H   ILE A 149      21.926  -5.890 -11.012  1.00  0.00      A    H  
+ATOM    381  HA  ILE A 149      23.959  -7.567  -9.988  1.00  0.00      A    H  
+ATOM    382  HB  ILE A 149      24.168  -5.103 -10.300  1.00  0.00      A    H  
+ATOM    383 HG12 ILE A 149      25.438  -4.445  -8.546  1.00  0.00      A    H  
+ATOM    384 HG13 ILE A 149      25.023  -5.893  -7.543  1.00  0.00      A    H  
+ATOM    385 HG21 ILE A 149      21.919  -4.438  -9.268  1.00  0.00      A    H  
+ATOM    386 HG22 ILE A 149      22.621  -4.931  -7.664  1.00  0.00      A    H  
+ATOM    387 HG23 ILE A 149      23.395  -3.555  -8.489  1.00  0.00      A    H  
+ATOM    388 HD11 ILE A 149      27.256  -5.930  -8.735  1.00  0.00      A    H  
+ATOM    389 HD12 ILE A 149      26.281  -7.395  -9.176  1.00  0.00      A    H  
+ATOM    390 HD13 ILE A 149      26.459  -6.039 -10.345  1.00  0.00      A    H  
+ATOM    391  N   LYS A 150      23.424  -8.152  -7.572  1.00  0.00      A    N  
+ATOM    392  CA  LYS A 150      22.927  -8.649  -6.291  1.00  0.00      A    C  
+ATOM    393  C   LYS A 150      24.215  -9.065  -5.536  1.00  0.00      A    C  
+ATOM    394  O   LYS A 150      25.084  -9.680  -6.082  1.00  0.00      A    O  
+ATOM    395  CB  LYS A 150      22.004  -9.857  -6.458  1.00  0.00      A    C  
+ATOM    396  CG  LYS A 150      21.455 -10.509  -5.208  1.00  0.00      A    C  
+ATOM    397  CD  LYS A 150      20.460 -11.555  -5.553  1.00  0.00      A    C  
+ATOM    398  CE  LYS A 150      21.133 -12.864  -6.145  1.00  0.00      A    C  
+ATOM    399  NZ  LYS A 150      19.975 -13.691  -6.566  1.00  0.00      A    N  
+ATOM    400  H   LYS A 150      24.352  -8.402  -7.839  1.00  0.00      A    H  
+ATOM    401  HA  LYS A 150      22.438  -7.846  -5.761  1.00  0.00      A    H  
+ATOM    402  HB2 LYS A 150      21.086  -9.614  -7.035  1.00  0.00      A    H  
+ATOM    403  HB3 LYS A 150      22.537 -10.601  -7.089  1.00  0.00      A    H  
+ATOM    404  HG2 LYS A 150      22.204 -10.900  -4.486  1.00  0.00      A    H  
+ATOM    405  HG3 LYS A 150      20.780  -9.851  -4.620  1.00  0.00      A    H  
+ATOM    406  HD2 LYS A 150      19.959 -11.845  -4.605  1.00  0.00      A    H  
+ATOM    407  HD3 LYS A 150      19.728 -11.120  -6.267  1.00  0.00      A    H  
+ATOM    408  HE2 LYS A 150      21.853 -12.704  -6.975  1.00  0.00      A    H  
+ATOM    409  HE3 LYS A 150      21.736 -13.453  -5.420  1.00  0.00      A    H  
+ATOM    410  HZ1 LYS A 150      19.549 -14.075  -5.698  1.00  0.00      A    H  
+ATOM    411  HZ2 LYS A 150      19.307 -13.055  -7.046  1.00  0.00      A    H  
+ATOM    412  HZ3 LYS A 150      20.279 -14.479  -7.172  1.00  0.00      A    H  
+ATOM    413  N   GLY A 151      24.432  -8.646  -4.233  1.00  0.00      A    N  
+ATOM    414  CA  GLY A 151      25.589  -9.095  -3.462  1.00  0.00      A    C  
+ATOM    415  C   GLY A 151      25.202 -10.262  -2.466  1.00  0.00      A    C  
+ATOM    416  O   GLY A 151      26.072 -10.750  -1.760  1.00  0.00      A    O  
+ATOM    417  H   GLY A 151      24.009  -7.868  -3.775  1.00  0.00      A    H  
+ATOM    418  HA2 GLY A 151      26.081  -8.261  -2.983  1.00  0.00      A    H  
+ATOM    419  HA3 GLY A 151      26.296  -9.597  -4.107  1.00  0.00      A    H  
+ATOM    420  N   THR A 152      23.912 -10.565  -2.367  1.00  0.00      A    N  
+ATOM    421  CA  THR A 152      23.472 -11.595  -1.501  1.00  0.00      A    C  
+ATOM    422  C   THR A 152      22.815 -12.661  -2.246  1.00  0.00      A    C  
+ATOM    423  O   THR A 152      21.717 -12.439  -2.718  1.00  0.00      A    O  
+ATOM    424  CB  THR A 152      22.466 -11.133  -0.417  1.00  0.00      A    C  
+ATOM    425  OG1 THR A 152      22.809  -9.853   0.001  1.00  0.00      A    O  
+ATOM    426  CG2 THR A 152      22.471 -12.057   0.802  1.00  0.00      A    C  
+ATOM    427  H   THR A 152      23.211 -10.076  -2.881  1.00  0.00      A    H  
+ATOM    428  HA  THR A 152      24.269 -11.989  -0.887  1.00  0.00      A    H  
+ATOM    429  HB  THR A 152      21.408 -11.158  -0.754  1.00  0.00      A    H  
+ATOM    430  HG1 THR A 152      22.626  -9.364  -0.805  1.00  0.00      A    H  
+ATOM    431 HG21 THR A 152      22.324 -13.118   0.506  1.00  0.00      A    H  
+ATOM    432 HG22 THR A 152      23.472 -12.023   1.283  1.00  0.00      A    H  
+ATOM    433 HG23 THR A 152      21.576 -11.870   1.433  1.00  0.00      A    H  
+ATOM    434  N   GLY A 153      23.477 -13.798  -2.371  1.00  0.00      A    N  
+ATOM    435  CA  GLY A 153      23.275 -14.925  -3.272  1.00  0.00      A    C  
+ATOM    436  C   GLY A 153      22.496 -16.047  -2.684  1.00  0.00      A    C  
+ATOM    437  O   GLY A 153      21.427 -15.830  -2.144  1.00  0.00      A    O  
+ATOM    438  H   GLY A 153      24.287 -13.974  -1.816  1.00  0.00      A    H  
+ATOM    439  HA2 GLY A 153      24.243 -15.316  -3.548  1.00  0.00      A    H  
+ATOM    440  HA3 GLY A 153      22.677 -14.576  -4.101  1.00  0.00      A    H  
+ATOM    441  N   VAL A 154      22.930 -17.328  -2.887  1.00  0.00      A    N  
+ATOM    442  CA  VAL A 154      21.984 -18.385  -2.591  1.00  0.00      A    C  
+ATOM    443  C   VAL A 154      21.842 -18.608  -1.063  1.00  0.00      A    C  
+ATOM    444  O   VAL A 154      22.794 -18.444  -0.296  1.00  0.00      A    O  
+ATOM    445  CB  VAL A 154      22.391 -19.648  -3.288  1.00  0.00      A    C  
+ATOM    446  CG1 VAL A 154      21.593 -20.947  -2.932  1.00  0.00      A    C  
+ATOM    447  CG2 VAL A 154      22.270 -19.250  -4.752  1.00  0.00      A    C  
+ATOM    448  H   VAL A 154      23.817 -17.615  -3.240  1.00  0.00      A    H  
+ATOM    449  HA  VAL A 154      21.062 -18.140  -3.097  1.00  0.00      A    H  
+ATOM    450  HB  VAL A 154      23.482 -19.852  -3.257  1.00  0.00      A    H  
+ATOM    451 HG11 VAL A 154      21.900 -21.783  -3.596  1.00  0.00      A    H  
+ATOM    452 HG12 VAL A 154      21.791 -21.262  -1.885  1.00  0.00      A    H  
+ATOM    453 HG13 VAL A 154      20.510 -20.741  -3.072  1.00  0.00      A    H  
+ATOM    454 HG21 VAL A 154      22.391 -20.186  -5.339  1.00  0.00      A    H  
+ATOM    455 HG22 VAL A 154      21.292 -18.770  -4.968  1.00  0.00      A    H  
+ATOM    456 HG23 VAL A 154      23.047 -18.476  -4.926  1.00  0.00      A    H  
+ATOM    457  N   GLY A 155      20.670 -18.879  -0.537  1.00  0.00      A    N  
+ATOM    458  CA  GLY A 155      20.462 -19.118   0.874  1.00  0.00      A    C  
+ATOM    459  C   GLY A 155      20.487 -17.919   1.756  1.00  0.00      A    C  
+ATOM    460  O   GLY A 155      20.401 -18.084   2.963  1.00  0.00      A    O  
+ATOM    461  H   GLY A 155      19.926 -19.039  -1.181  1.00  0.00      A    H  
+ATOM    462  HA2 GLY A 155      21.117 -19.871   1.287  1.00  0.00      A    H  
+ATOM    463  HA3 GLY A 155      19.496 -19.588   0.986  1.00  0.00      A    H  
+ATOM    464  N   GLY A 156      20.566 -16.676   1.198  1.00  0.00      A    N  
+ATOM    465  CA  GLY A 156      20.723 -15.470   1.979  1.00  0.00      A    C  
+ATOM    466  C   GLY A 156      22.131 -15.258   2.394  1.00  0.00      A    C  
+ATOM    467  O   GLY A 156      22.425 -14.303   3.132  1.00  0.00      A    O  
+ATOM    468  H   GLY A 156      20.557 -16.688   0.201  1.00  0.00      A    H  
+ATOM    469  HA2 GLY A 156      20.205 -15.571   2.921  1.00  0.00      A    H  
+ATOM    470  HA3 GLY A 156      20.379 -14.636   1.386  1.00  0.00      A    H  
+ATOM    471  N   ARG A 157      23.060 -16.033   1.825  1.00  0.00      A    N  
+ATOM    472  CA  ARG A 157      24.449 -15.991   2.225  1.00  0.00      A    C  
+ATOM    473  C   ARG A 157      25.265 -15.035   1.312  1.00  0.00      A    C  
+ATOM    474  O   ARG A 157      25.093 -15.130   0.101  1.00  0.00      A    O  
+ATOM    475  CB  ARG A 157      24.950 -17.387   2.294  1.00  0.00      A    C  
+ATOM    476  CG  ARG A 157      24.255 -18.480   3.149  1.00  0.00      A    C  
+ATOM    477  CD  ARG A 157      24.698 -19.941   3.030  1.00  0.00      A    C  
+ATOM    478  NE  ARG A 157      24.285 -20.297   1.608  1.00  0.00      A    N  
+ATOM    479  CZ  ARG A 157      23.592 -21.427   1.267  1.00  0.00      A    C  
+ATOM    480  NH1 ARG A 157      23.045 -22.252   2.220  1.00  0.00      A    N  
+ATOM    481  NH2 ARG A 157      23.460 -21.768   0.002  1.00  0.00      A    N  
+ATOM    482  H   ARG A 157      22.805 -16.776   1.212  1.00  0.00      A    H  
+ATOM    483  HA  ARG A 157      24.517 -15.542   3.205  1.00  0.00      A    H  
+ATOM    484  HB2 ARG A 157      25.079 -17.854   1.294  1.00  0.00      A    H  
+ATOM    485  HB3 ARG A 157      25.904 -17.322   2.859  1.00  0.00      A    H  
+ATOM    486  HG2 ARG A 157      24.499 -18.178   4.189  1.00  0.00      A    H  
+ATOM    487  HG3 ARG A 157      23.161 -18.354   3.006  1.00  0.00      A    H  
+ATOM    488  HD2 ARG A 157      25.806 -20.010   3.054  1.00  0.00      A    H  
+ATOM    489  HD3 ARG A 157      24.096 -20.544   3.743  1.00  0.00      A    H  
+ATOM    490  HE  ARG A 157      24.517 -19.714   0.829  1.00  0.00      A    H  
+ATOM    491 HH11 ARG A 157      22.733 -21.747   3.024  1.00  0.00      A    H  
+ATOM    492 HH12 ARG A 157      22.433 -22.978   1.906  1.00  0.00      A    H  
+ATOM    493 HH21 ARG A 157      23.932 -21.178  -0.653  1.00  0.00      A    H  
+ATOM    494 HH22 ARG A 157      23.161 -22.692  -0.236  1.00  0.00      A    H  
+ATOM    495  N   LEU A 158      26.030 -14.089   1.880  1.00  0.00      A    N  
+ATOM    496  CA  LEU A 158      26.794 -13.198   1.023  1.00  0.00      A    C  
+ATOM    497  C   LEU A 158      27.763 -13.855   0.095  1.00  0.00      A    C  
+ATOM    498  O   LEU A 158      28.547 -14.756   0.450  1.00  0.00      A    O  
+ATOM    499  CB  LEU A 158      27.596 -12.175   1.939  1.00  0.00      A    C  
+ATOM    500  CG  LEU A 158      26.735 -11.099   2.480  1.00  0.00      A    C  
+ATOM    501  CD1 LEU A 158      27.477 -10.199   3.511  1.00  0.00      A    C  
+ATOM    502  CD2 LEU A 158      26.165 -10.110   1.423  1.00  0.00      A    C  
+ATOM    503  H   LEU A 158      26.174 -14.130   2.866  1.00  0.00      A    H  
+ATOM    504  HA  LEU A 158      26.120 -12.647   0.385  1.00  0.00      A    H  
+ATOM    505  HB2 LEU A 158      28.057 -12.807   2.728  1.00  0.00      A    H  
+ATOM    506  HB3 LEU A 158      28.342 -11.655   1.301  1.00  0.00      A    H  
+ATOM    507  HG  LEU A 158      25.833 -11.521   2.973  1.00  0.00      A    H  
+ATOM    508 HD11 LEU A 158      26.788  -9.523   4.061  1.00  0.00      A    H  
+ATOM    509 HD12 LEU A 158      28.027 -10.816   4.254  1.00  0.00      A    H  
+ATOM    510 HD13 LEU A 158      28.134  -9.455   3.012  1.00  0.00      A    H  
+ATOM    511 HD21 LEU A 158      25.305 -10.512   0.845  1.00  0.00      A    H  
+ATOM    512 HD22 LEU A 158      25.959  -9.208   2.038  1.00  0.00      A    H  
+ATOM    513 HD23 LEU A 158      26.976  -9.809   0.725  1.00  0.00      A    H  
+ATOM    514  N   THR A 159      27.768 -13.320  -1.216  1.00  0.00      A    N  
+ATOM    515  CA  THR A 159      28.492 -13.952  -2.333  1.00  0.00      A    C  
+ATOM    516  C   THR A 159      29.976 -13.573  -2.252  1.00  0.00      A    C  
+ATOM    517  O   THR A 159      30.319 -12.423  -1.910  1.00  0.00      A    O  
+ATOM    518  CB  THR A 159      27.804 -13.547  -3.601  1.00  0.00      A    C  
+ATOM    519  OG1 THR A 159      26.414 -13.866  -3.602  1.00  0.00      A    O  
+ATOM    520  CG2 THR A 159      28.549 -14.091  -4.822  1.00  0.00      A    C  
+ATOM    521  H   THR A 159      27.273 -12.474  -1.396  1.00  0.00      A    H  
+ATOM    522  HA  THR A 159      28.343 -15.019  -2.260  1.00  0.00      A    H  
+ATOM    523  HB  THR A 159      27.990 -12.452  -3.595  1.00  0.00      A    H  
+ATOM    524  HG1 THR A 159      25.965 -13.383  -4.300  1.00  0.00      A    H  
+ATOM    525 HG21 THR A 159      27.904 -13.986  -5.720  1.00  0.00      A    H  
+ATOM    526 HG22 THR A 159      29.373 -13.367  -4.998  1.00  0.00      A    H  
+ATOM    527 HG23 THR A 159      28.901 -15.141  -4.728  1.00  0.00      A    H  
+ATOM    528  N   ARG A 160      30.850 -14.614  -2.377  1.00  0.00      A    N  
+ATOM    529  CA  ARG A 160      32.251 -14.508  -2.141  1.00  0.00      A    C  
+ATOM    530  C   ARG A 160      32.866 -15.844  -2.668  1.00  0.00      A    C  
+ATOM    531  O   ARG A 160      32.166 -16.885  -2.938  1.00  0.00      A    O  
+ATOM    532  CB  ARG A 160      32.515 -14.247  -0.641  1.00  0.00      A    C  
+ATOM    533  CG  ARG A 160      31.906 -15.350   0.283  1.00  0.00      A    C  
+ATOM    534  CD  ARG A 160      31.898 -14.910   1.738  1.00  0.00      A    C  
+ATOM    535  NE  ARG A 160      31.832 -16.153   2.496  1.00  0.00      A    N  
+ATOM    536  CZ  ARG A 160      30.729 -16.851   2.654  1.00  0.00      A    C  
+ATOM    537  NH1 ARG A 160      29.502 -16.493   2.181  1.00  0.00      A    N  
+ATOM    538  NH2 ARG A 160      30.712 -17.868   3.516  1.00  0.00      A    N  
+ATOM    539  H   ARG A 160      30.569 -15.483  -2.777  1.00  0.00      A    H  
+ATOM    540  HA  ARG A 160      32.607 -13.642  -2.679  1.00  0.00      A    H  
+ATOM    541  HB2 ARG A 160      33.617 -14.295  -0.505  1.00  0.00      A    H  
+ATOM    542  HB3 ARG A 160      32.112 -13.283  -0.261  1.00  0.00      A    H  
+ATOM    543  HG2 ARG A 160      30.858 -15.417  -0.077  1.00  0.00      A    H  
+ATOM    544  HG3 ARG A 160      32.265 -16.372   0.037  1.00  0.00      A    H  
+ATOM    545  HD2 ARG A 160      32.841 -14.444   2.096  1.00  0.00      A    H  
+ATOM    546  HD3 ARG A 160      31.048 -14.230   1.960  1.00  0.00      A    H  
+ATOM    547  HE  ARG A 160      32.661 -16.494   2.940  1.00  0.00      A    H  
+ATOM    548 HH11 ARG A 160      29.405 -15.731   1.540  1.00  0.00      A    H  
+ATOM    549 HH12 ARG A 160      28.692 -16.965   2.527  1.00  0.00      A    H  
+ATOM    550 HH21 ARG A 160      31.483 -17.950   4.148  1.00  0.00      A    H  
+ATOM    551 HH22 ARG A 160      29.853 -18.326   3.746  1.00  0.00      A    H  
+ATOM    552  N   GLU A 161      34.179 -15.835  -3.029  1.00  0.00      A    N  
+ATOM    553  CA  GLU A 161      34.990 -16.890  -3.695  1.00  0.00      A    C  
+ATOM    554  C   GLU A 161      35.046 -18.210  -2.964  1.00  0.00      A    C  
+ATOM    555  O   GLU A 161      34.949 -18.305  -1.715  1.00  0.00      A    O  
+ATOM    556  CB  GLU A 161      36.417 -16.455  -3.828  1.00  0.00      A    C  
+ATOM    557  CG  GLU A 161      37.096 -16.071  -2.391  1.00  0.00      A    C  
+ATOM    558  CD  GLU A 161      38.524 -15.712  -2.548  1.00  0.00      A    C  
+ATOM    559  OE1 GLU A 161      39.025 -15.127  -1.561  1.00  0.00      A    O  
+ATOM    560  OE2 GLU A 161      39.174 -15.970  -3.609  1.00  0.00      A    O  
+ATOM    561  H   GLU A 161      34.712 -15.026  -2.794  1.00  0.00      A    H  
+ATOM    562  HA  GLU A 161      34.482 -17.002  -4.642  1.00  0.00      A    H  
+ATOM    563  HB2 GLU A 161      36.969 -17.312  -4.268  1.00  0.00      A    H  
+ATOM    564  HB3 GLU A 161      36.679 -15.693  -4.593  1.00  0.00      A    H  
+ATOM    565  HG2 GLU A 161      36.625 -15.158  -1.968  1.00  0.00      A    H  
+ATOM    566  HG3 GLU A 161      37.037 -16.867  -1.617  1.00  0.00      A    H  
+ATOM    567  N   ASP A 162      34.988 -19.331  -3.723  1.00  0.00      A    N  
+ATOM    568  CA  ASP A 162      34.844 -20.691  -3.245  1.00  0.00      A    C  
+ATOM    569  C   ASP A 162      36.237 -21.265  -3.090  1.00  0.00      A    C  
+ATOM    570  O   ASP A 162      36.927 -21.523  -4.061  1.00  0.00      A    O  
+ATOM    571  CB  ASP A 162      33.982 -21.590  -4.190  1.00  0.00      A    C  
+ATOM    572  CG  ASP A 162      32.623 -21.026  -4.187  1.00  0.00      A    C  
+ATOM    573  OD1 ASP A 162      32.147 -20.634  -3.070  1.00  0.00      A    O  
+ATOM    574  OD2 ASP A 162      32.007 -20.866  -5.235  1.00  0.00      A    O  
+ATOM    575  H   ASP A 162      35.079 -19.288  -4.715  1.00  0.00      A    H  
+ATOM    576  HA  ASP A 162      34.460 -20.672  -2.235  1.00  0.00      A    H  
+ATOM    577  HB2 ASP A 162      34.482 -21.529  -5.180  1.00  0.00      A    H  
+ATOM    578  HB3 ASP A 162      33.916 -22.649  -3.858  1.00  0.00      A    H  
+ATOM    579  N   VAL A 163      36.695 -21.414  -1.843  1.00  0.00      A    N  
+ATOM    580  CA  VAL A 163      38.011 -21.848  -1.488  1.00  0.00      A    C  
+ATOM    581  C   VAL A 163      38.110 -23.264  -1.558  1.00  0.00      A    C  
+ATOM    582  O   VAL A 163      37.130 -23.989  -1.326  1.00  0.00      A    O  
+ATOM    583  CB  VAL A 163      38.432 -21.356  -0.110  1.00  0.00      A    C  
+ATOM    584  CG1 VAL A 163      38.503 -19.825   0.013  1.00  0.00      A    C  
+ATOM    585  CG2 VAL A 163      37.498 -21.881   0.959  1.00  0.00      A    C  
+ATOM    586  H   VAL A 163      36.064 -21.351  -1.074  1.00  0.00      A    H  
+ATOM    587  HA  VAL A 163      38.761 -21.613  -2.229  1.00  0.00      A    H  
+ATOM    588  HB  VAL A 163      39.409 -21.795   0.188  1.00  0.00      A    H  
+ATOM    589 HG11 VAL A 163      37.468 -19.450   0.157  1.00  0.00      A    H  
+ATOM    590 HG12 VAL A 163      38.946 -19.520   0.985  1.00  0.00      A    H  
+ATOM    591 HG13 VAL A 163      39.003 -19.264  -0.805  1.00  0.00      A    H  
+ATOM    592 HG21 VAL A 163      37.668 -22.969   1.102  1.00  0.00      A    H  
+ATOM    593 HG22 VAL A 163      37.792 -21.419   1.926  1.00  0.00      A    H  
+ATOM    594 HG23 VAL A 163      36.415 -21.739   0.753  1.00  0.00      A    H  
+ATOM    595  N   GLU A 164      39.312 -23.847  -1.816  1.00  0.00      A    N  
+ATOM    596  CA  GLU A 164      39.563 -25.296  -1.630  1.00  0.00      A    C  
+ATOM    597  C   GLU A 164      40.185 -25.475  -0.306  1.00  0.00      A    C  
+ATOM    598  O   GLU A 164      41.023 -24.721   0.174  1.00  0.00      A    O  
+ATOM    599  CB  GLU A 164      40.455 -25.714  -2.766  1.00  0.00      A    C  
+ATOM    600  CG  GLU A 164      40.929 -27.166  -2.834  1.00  0.00      A    C  
+ATOM    601  CD  GLU A 164      41.492 -27.553  -4.165  1.00  0.00      A    C  
+ATOM    602  OE1 GLU A 164      40.925 -28.488  -4.804  1.00  0.00      A    O  
+ATOM    603  OE2 GLU A 164      42.436 -26.890  -4.549  1.00  0.00      A    O  
+ATOM    604  H   GLU A 164      40.129 -23.275  -1.813  1.00  0.00      A    H  
+ATOM    605  HA  GLU A 164      38.646 -25.860  -1.718  1.00  0.00      A    H  
+ATOM    606  HB2 GLU A 164      39.878 -25.381  -3.655  1.00  0.00      A    H  
+ATOM    607  HB3 GLU A 164      41.319 -25.019  -2.700  1.00  0.00      A    H  
+ATOM    608  HG2 GLU A 164      41.644 -27.243  -1.988  1.00  0.00      A    H  
+ATOM    609  HG3 GLU A 164      40.025 -27.803  -2.728  1.00  0.00      A    H  
+ATOM    610  N   LYS A 165      39.818 -26.591   0.329  1.00  0.00      A    N  
+ATOM    611  CA  LYS A 165      40.227 -27.195   1.541  1.00  0.00      A    C  
+ATOM    612  C   LYS A 165      41.507 -28.047   1.318  1.00  0.00      A    C  
+ATOM    613  O   LYS A 165      41.554 -28.760   0.325  1.00  0.00      A    O  
+ATOM    614  CB  LYS A 165      39.052 -27.981   2.209  1.00  0.00      A    C  
+ATOM    615  CG  LYS A 165      39.197 -28.116   3.761  1.00  0.00      A    C  
+ATOM    616  CD  LYS A 165      38.115 -28.943   4.435  1.00  0.00      A    C  
+ATOM    617  CE  LYS A 165      36.736 -28.410   4.133  1.00  0.00      A    C  
+ATOM    618  NZ  LYS A 165      35.709 -29.143   4.962  1.00  0.00      A    N  
+ATOM    619  H   LYS A 165      39.204 -27.185  -0.186  1.00  0.00      A    H  
+ATOM    620  HA  LYS A 165      40.533 -26.407   2.213  1.00  0.00      A    H  
+ATOM    621  HB2 LYS A 165      38.242 -27.227   2.111  1.00  0.00      A    H  
+ATOM    622  HB3 LYS A 165      38.836 -28.955   1.718  1.00  0.00      A    H  
+ATOM    623  HG2 LYS A 165      40.149 -28.661   3.942  1.00  0.00      A    H  
+ATOM    624  HG3 LYS A 165      39.294 -27.083   4.158  1.00  0.00      A    H  
+ATOM    625  HD2 LYS A 165      38.170 -29.991   4.071  1.00  0.00      A    H  
+ATOM    626  HD3 LYS A 165      38.295 -29.094   5.521  1.00  0.00      A    H  
+ATOM    627  HE2 LYS A 165      36.784 -27.381   4.549  1.00  0.00      A    H  
+ATOM    628  HE3 LYS A 165      36.505 -28.473   3.048  1.00  0.00      A    H  
+ATOM    629  HZ1 LYS A 165      35.589 -30.144   4.708  1.00  0.00      A    H  
+ATOM    630  HZ2 LYS A 165      35.833 -29.145   5.995  1.00  0.00      A    H  
+ATOM    631  HZ3 LYS A 165      34.815 -28.612   4.946  1.00  0.00      A    H  
+ATOM    632  N   HIS A 166      42.582 -27.949   2.164  1.00  0.00      A    N  
+ATOM    633  CA  HIS A 166      43.794 -28.673   2.005  1.00  0.00      A    C  
+ATOM    634  C   HIS A 166      43.699 -30.190   1.885  1.00  0.00      A    C  
+ATOM    635  O   HIS A 166      42.790 -30.774   2.456  1.00  0.00      A    O  
+ATOM    636  CB  HIS A 166      42.574 -27.400   2.997  1.00  0.00      A    C  
+ATOM    637  CG  HIS A 166      44.268 -28.349   1.090  1.00  0.00      A    C  
+ATOM    638  ND1 HIS A 166      44.595 -30.884   1.103  1.00  0.00      A    N  
+ATOM    639  CD2 HIS A 166      44.445 -32.344   0.881  1.00  0.00      A    C  
+ATOM    640  CE1 HIS A 166      44.968 -33.236   2.052  1.00  0.00      A    C  
+ATOM    641  NE2 HIS A 166      44.919 -34.436   2.052  1.00  0.00      A    N  
+ATOM    642  H   HIS A 166      45.251 -32.777  -0.401  1.00  0.00      A    H  
+ATOM    643  HA  HIS A 166      46.703 -32.461  -0.321  1.00  0.00      A    H  
+ATOM    644  HB2 HIS A 166      47.648 -33.506  -0.943  1.00  0.00      A    H  
+ATOM    645  HB3 HIS A 166      46.965 -31.179  -1.157  1.00  0.00      A    H  
+ATOM    646  HD1 HIS A 166      45.290 -30.378   0.598  1.00  0.00      A    H  
+ATOM    647  HD2 HIS A 166      43.436 -32.663   0.666  1.00  0.00      A    H  
+ATOM    648  HE1 HIS A 166      45.238 -33.880  -0.538  1.00  0.00      A    H  
+ATOM    649  HE2 HIS A 166      44.788 -32.269  -1.273  1.00  0.00      A    H  
+ATOM    650  N   LEU A 167      46.963 -32.119   0.703  1.00  0.00      A    N  
+ATOM    651  CA  LEU A 167      48.673 -33.079  -0.907  1.00  0.00      A    C  
+ATOM    652  C   LEU A 167      47.710 -34.439  -0.343  1.00  0.00      A    C  
+ATOM    653  O   LEU A 167      47.311 -33.662  -1.990  1.00  0.00      A    O  
+ATOM    654  CB  LEU A 167      47.992 -30.766  -1.056  1.00  0.00      A    C  
+ATOM    655  CG  LEU A 167      46.756 -31.434  -2.218  1.00  0.00      A    C  
+ATOM    656  CD1 LEU A 167      46.250 -30.384  -0.855  1.00  0.00      A    C  
+ATOM    657  CD2 LEU A 167      45.405 -32.605   3.125  1.00  0.00      A    C  
+ATOM    658  H   LEU A 167      46.104 -33.169   4.219  1.00  0.00      A    H  
+ATOM    659  HA  LEU A 167      45.705 -32.478   5.476  1.00  0.00      A    H  
+ATOM    660  HB2 LEU A 167      45.585 -31.247   5.639  1.00  0.00      A    H  
+ATOM    661  HB3 LEU A 167      47.647 -33.170   3.940  1.00  0.00      A    H  
+ATOM    662  HG  LEU A 167      45.169 -31.643   3.244  1.00  0.00      A    H  
+ATOM    663 HD11 LEU A 167      45.819 -34.184   4.458  1.00  0.00      A    H  
+ATOM    664 HD12 LEU A 167      48.104 -32.163   3.832  1.00  0.00      A    H  
+ATOM    665 HD13 LEU A 167      47.782 -33.966   3.176  1.00  0.00      A    H  
+ATOM    666 HD21 LEU A 167      48.113 -33.641   4.831  1.00  0.00      A    H  
+ATOM    667 HD22 LEU A 167      45.490 -33.311   6.543  1.00  0.00      A    H  
+ATOM    668 HD23 LEU A 167      45.195 -32.925   7.855  1.00  0.00      A    H  
+ATOM    669  N   ALA A 168      43.939 -32.192   8.221  1.00  0.00      A    N  
+ATOM    670  CA  ALA A 168      43.863 -31.474   9.199  1.00  0.00      A    C  
+ATOM    671  C   ALA A 168      46.451 -32.367   8.557  1.00  0.00      A    C  
+ATOM    672  O   ALA A 168      47.665 -33.314   8.652  1.00  0.00      A    O  
+ATOM    673  CB  ALA A 168      48.902 -32.764   9.306  1.00  0.00      A    C  
+ATOM    674  H   ALA A 168      50.227 -33.217   8.851  1.00  0.00      A    H  
+ATOM    675  HA  ALA A 168      50.547 -34.551   9.456  1.00  0.00      A    H  
+ATOM    676  HB1 ALA A 168      45.462 -34.305   6.464  1.00  0.00      A    H  
+ATOM    677  HB2 ALA A 168      44.953 -33.866   8.327  1.00  0.00      A    H  
+ATOM    678  HB3 ALA A 168      46.839 -31.465   8.037  1.00  0.00      A    H  
+ATOM    679  N   LYS A 169      46.225 -32.006   9.583  1.00  0.00      A    N  
+ATOM    680  CA  LYS A 169      47.407 -34.288   9.121  1.00  0.00      A    C  
+ATOM    681  C   LYS A 169      47.952 -33.609   7.621  1.00  0.00      A    C  
+ATOM    682  O   LYS A 169      48.912 -31.693   9.011  1.00  0.00      A    O  
+ATOM    683  CB  LYS A 169      48.811 -32.747  10.413  1.00  0.00      A    C  
+ATOM    684  CG  LYS A 169      50.181 -33.422   7.760  1.00  0.00      A    C  
+ATOM    685  CD  LYS A 169      50.977 -32.483   9.216  1.00  0.00      A    C  
+ATOM    686  CE  LYS A 169      50.008 -35.352   9.069  1.00  0.00      A    C  
+ATOM    687  NZ  LYS A 169      51.550 -34.795   9.582  1.00  0.00      A    N  
+ATOM    688  H   LYS A 169      50.213 -34.374  10.424  1.00  0.00      A    H  
+ATOM    689  HA  LYS A 169      42.902 -32.282   7.413  1.00  0.00      A    H  
+ATOM    690  HB2 LYS A 169      41.617 -31.640   7.644  1.00  0.00      A    H  
+ATOM    691  HB3 LYS A 169      40.535 -32.686   7.777  1.00  0.00      A    H  
+ATOM    692  HG2 LYS A 169      40.592 -33.712   7.092  1.00  0.00      A    H  
+ATOM    693  HG3 LYS A 169      41.149 -30.748   6.485  1.00  0.00      A    H  
+ATOM    694  HD2 LYS A 169      39.479 -32.423   8.408  1.00  0.00      A    H  
+ATOM    695  HD3 LYS A 169      42.878 -32.764   6.541  1.00  0.00      A    H  
+ATOM    696  HE2 LYS A 169      41.644 -31.027   8.533  1.00  0.00      A    H  
+ATOM    697  HE3 LYS A 169      40.160 -30.282   6.686  1.00  0.00      A    H  
+ATOM    698  HZ1 LYS A 169      40.969 -31.238   5.504  1.00  0.00      A    H  
+ATOM    699  HZ2 LYS A 169      41.931 -29.988   6.270  1.00  0.00      A    H  
+ATOM    700  HZ3 LYS A 169      44.885 -28.326   3.002  1.00  0.00      A    H  
+ATOM    701  N   ALA A 170      46.334 -28.790   2.681  1.00  0.00      A    N  
+ATOM    702  CA  ALA A 170      46.879 -28.412   1.451  1.00  0.00      A    C  
+ATOM    703  C   ALA A 170      47.274 -29.487   3.401  1.00  0.00      A    C  
+ATOM    704  O   ALA A 170      48.099 -29.008   1.405  1.00  0.00      A    O  
+ATOM    705  CB  ALA A 170      48.414 -29.555   2.605  1.00  0.00      A    C  
+ATOM    706  OXT ALA A 170      44.962 -27.218   2.975  1.00  0.00      A    O  
+ATOM    707  H   ALA A 170      44.538 -28.658   4.004  1.00  0.00      A    H  
+ATOM    708  HA  ALA A 170      47.368 -29.678   4.463  1.00  0.00      A    H  
+ATOM    709  HB1 ALA A 170      48.911 -28.743   0.728  1.00  0.00      A    H  
+ATOM    710  HB2 ALA A 170      49.336 -29.822   2.884  1.00  0.00      A    H 
+ATOM    711  HB3 ALA A 170      47.800 -30.200   2.700  1.00  0.00      A    H  
+ENDMDL
+END

entangled-tps/data/chignolin/folded.pdb

@@ -0,0 +1,280 @@
+COMPND    chignolin_folded.pdb 
+AUTHOR    GENERATED BY OPEN BABEL 3.1.1
+ATOM      1  N   GLY A   1      -6.986   1.003   3.359  1.00  0.00           N  
+ATOM      2  CA  GLY A   1      -6.740  -0.436   3.053  1.00  0.00           C  
+ATOM      3  C   GLY A   1      -5.453  -0.575   2.240  1.00  0.00           C  
+ATOM      4  O   GLY A   1      -4.472  -1.123   2.702  1.00  0.00           O  
+ATOM      5  H1  GLY A   1      -6.931   1.558   2.483  1.00  0.00           H  
+ATOM      6  H2  GLY A   1      -6.265   1.342   4.030  1.00  0.00           H  
+ATOM      7  H3  GLY A   1      -7.930   1.112   3.779  1.00  0.00           H  
+ATOM      8  HA2 GLY A   1      -6.645  -0.987   3.978  1.00  0.00           H  
+ATOM      9  HA3 GLY A   1      -7.567  -0.829   2.482  1.00  0.00           H  
+ATOM     10  N   TYR A   2      -5.446  -0.085   1.032  1.00  0.00           N  
+ATOM     11  CA  TYR A   2      -4.221  -0.193   0.191  1.00  0.00           C  
+ATOM     12  C   TYR A   2      -3.136   0.733   0.742  1.00  0.00           C  
+ATOM     13  O   TYR A   2      -3.289   1.939   0.768  1.00  0.00           O  
+ATOM     14  CB  TYR A   2      -4.547   0.213  -1.247  1.00  0.00           C  
+ATOM     15  CG  TYR A   2      -3.286   0.169  -2.076  1.00  0.00           C  
+ATOM     16  CD1 TYR A   2      -2.899  -1.024  -2.700  1.00  0.00           C  
+ATOM     17  CD2 TYR A   2      -2.501   1.320  -2.221  1.00  0.00           C  
+ATOM     18  CE1 TYR A   2      -1.728  -1.066  -3.466  1.00  0.00           C  
+ATOM     19  CE2 TYR A   2      -1.331   1.277  -2.987  1.00  0.00           C  
+ATOM     20  CZ  TYR A   2      -0.944   0.085  -3.609  1.00  0.00           C  
+ATOM     21  OH  TYR A   2       0.210   0.044  -4.364  1.00  0.00           O  
+ATOM     22  H   TYR A   2      -6.249   0.353   0.675  1.00  0.00           H  
+ATOM     23  HA  TYR A   2      -3.865  -1.213   0.204  1.00  0.00           H  
+ATOM     24  HB2 TYR A   2      -5.275  -0.471  -1.658  1.00  0.00           H  
+ATOM     25  HB3 TYR A   2      -4.948   1.216  -1.255  1.00  0.00           H  
+ATOM     26  HD1 TYR A   2      -3.504  -1.913  -2.589  1.00  0.00           H  
+ATOM     27  HD2 TYR A   2      -2.799   2.240  -1.740  1.00  0.00           H  
+ATOM     28  HE1 TYR A   2      -1.429  -1.985  -3.945  1.00  0.00           H  
+ATOM     29  HE2 TYR A   2      -0.726   2.166  -3.098  1.00  0.00           H  
+ATOM     30  HH  TYR A   2       0.080  -0.594  -5.069  1.00  0.00           H  
+ATOM     31  N   ASP A   3      -2.037   0.182   1.177  1.00  0.00           N  
+ATOM     32  CA  ASP A   3      -0.940   1.032   1.718  1.00  0.00           C  
+ATOM     33  C   ASP A   3      -0.123   1.602   0.550  1.00  0.00           C  
+ATOM     34  O   ASP A   3       0.515   0.860  -0.169  1.00  0.00           O  
+ATOM     35  CB  ASP A   3      -0.030   0.183   2.608  1.00  0.00           C  
+ATOM     36  CG  ASP A   3       0.783   1.097   3.527  1.00  0.00           C  
+ATOM     37  OD1 ASP A   3       1.270   2.106   3.046  1.00  0.00           O  
+ATOM     38  OD2 ASP A   3       0.904   0.771   4.696  1.00  0.00           O  
+ATOM     39  H   ASP A   3      -1.929  -0.792   1.143  1.00  0.00           H  
+ATOM     40  HA  ASP A   3      -1.364   1.834   2.301  1.00  0.00           H  
+ATOM     41  HB2 ASP A   3      -0.633  -0.486   3.205  1.00  0.00           H  
+ATOM     42  HB3 ASP A   3       0.643  -0.392   1.990  1.00  0.00           H  
+ATOM     43  N   PRO A   4      -0.167   2.902   0.390  1.00  0.00           N  
+ATOM     44  CA  PRO A   4       0.563   3.590  -0.689  1.00  0.00           C  
+ATOM     45  C   PRO A   4       2.049   3.716  -0.336  1.00  0.00           C  
+ATOM     46  O   PRO A   4       2.907   3.662  -1.194  1.00  0.00           O  
+ATOM     47  CB  PRO A   4      -0.102   4.968  -0.753  1.00  0.00           C  
+ATOM     48  CG  PRO A   4      -0.765   5.195   0.626  1.00  0.00           C  
+ATOM     49  CD  PRO A   4      -0.947   3.805   1.262  1.00  0.00           C  
+ATOM     50  HA  PRO A   4       0.436   3.074  -1.627  1.00  0.00           H  
+ATOM     51  HB2 PRO A   4       0.642   5.729  -0.942  1.00  0.00           H  
+ATOM     52  HB3 PRO A   4      -0.856   4.981  -1.525  1.00  0.00           H  
+ATOM     53  HG2 PRO A   4      -0.125   5.809   1.246  1.00  0.00           H  
+ATOM     54  HG3 PRO A   4      -1.726   5.668   0.503  1.00  0.00           H  
+ATOM     55  HD2 PRO A   4      -0.551   3.796   2.269  1.00  0.00           H  
+ATOM     56  HD3 PRO A   4      -1.987   3.519   1.258  1.00  0.00           H  
+ATOM     57  N   GLU A   5       2.359   3.886   0.920  1.00  0.00           N  
+ATOM     58  CA  GLU A   5       3.789   4.014   1.322  1.00  0.00           C  
+ATOM     59  C   GLU A   5       4.498   2.675   1.111  1.00  0.00           C  
+ATOM     60  O   GLU A   5       5.499   2.593   0.427  1.00  0.00           O  
+ATOM     61  CB  GLU A   5       3.870   4.411   2.797  1.00  0.00           C  
+ATOM     62  CG  GLU A   5       3.427   5.866   2.958  1.00  0.00           C  
+ATOM     63  CD  GLU A   5       4.308   6.557   4.001  1.00  0.00           C  
+ATOM     64  OE1 GLU A   5       4.729   5.887   4.930  1.00  0.00           O  
+ATOM     65  OE2 GLU A   5       4.547   7.745   3.853  1.00  0.00           O  
+ATOM     66  H   GLU A   5       1.655   3.927   1.599  1.00  0.00           H  
+ATOM     67  HA  GLU A   5       4.265   4.773   0.718  1.00  0.00           H  
+ATOM     68  HB2 GLU A   5       3.224   3.770   3.379  1.00  0.00           H  
+ATOM     69  HB3 GLU A   5       4.888   4.307   3.143  1.00  0.00           H  
+ATOM     70  HG2 GLU A   5       3.519   6.378   2.012  1.00  0.00           H  
+ATOM     71  HG3 GLU A   5       2.397   5.895   3.284  1.00  0.00           H  
+ATOM     72  N   THR A   6       3.985   1.625   1.691  1.00  0.00           N  
+ATOM     73  CA  THR A   6       4.627   0.292   1.519  1.00  0.00           C  
+ATOM     74  C   THR A   6       4.208  -0.297   0.171  1.00  0.00           C  
+ATOM     75  O   THR A   6       4.872  -1.155  -0.378  1.00  0.00           O  
+ATOM     76  CB  THR A   6       4.180  -0.641   2.646  1.00  0.00           C  
+ATOM     77  OG1 THR A   6       4.472  -0.040   3.899  1.00  0.00           O  
+ATOM     78  CG2 THR A   6       4.921  -1.973   2.530  1.00  0.00           C  
+ATOM     79  H   THR A   6       3.174   1.712   2.236  1.00  0.00           H  
+ATOM     80  HA  THR A   6       5.701   0.402   1.546  1.00  0.00           H  
+ATOM     81  HB  THR A   6       3.118  -0.817   2.568  1.00  0.00           H  
+ATOM     82  HG1 THR A   6       4.471  -0.730   4.567  1.00  0.00           H  
+ATOM     83 HG21 THR A   6       4.207  -2.784   2.533  1.00  0.00           H  
+ATOM     84 HG22 THR A   6       5.594  -2.084   3.369  1.00  0.00           H  
+ATOM     85 HG23 THR A   6       5.485  -1.992   1.610  1.00  0.00           H  
+ATOM     86  N   GLY A   7       3.112   0.161  -0.368  1.00  0.00           N  
+ATOM     87  CA  GLY A   7       2.646  -0.365  -1.681  1.00  0.00           C  
+ATOM     88  C   GLY A   7       2.326  -1.855  -1.558  1.00  0.00           C  
+ATOM     89  O   GLY A   7       2.897  -2.681  -2.244  1.00  0.00           O  
+ATOM     90  H   GLY A   7       2.595   0.855   0.092  1.00  0.00           H  
+ATOM     91  HA2 GLY A   7       1.758   0.171  -1.988  1.00  0.00           H  
+ATOM     92  HA3 GLY A   7       3.421  -0.228  -2.419  1.00  0.00           H  
+ATOM     93  N   THR A   8       1.415  -2.209  -0.692  1.00  0.00           N  
+ATOM     94  CA  THR A   8       1.063  -3.648  -0.534  1.00  0.00           C  
+ATOM     95  C   THR A   8      -0.420  -3.781  -0.220  1.00  0.00           C  
+ATOM     96  O   THR A   8      -1.024  -2.913   0.377  1.00  0.00           O  
+ATOM     97  CB  THR A   8       1.884  -4.260   0.602  1.00  0.00           C  
+ATOM     98  OG1 THR A   8       3.116  -3.560   0.725  1.00  0.00           O  
+ATOM     99  CG2 THR A   8       2.158  -5.733   0.294  1.00  0.00           C  
+ATOM    100  H   THR A   8       0.964  -1.530  -0.150  1.00  0.00           H  
+ATOM    101  HA  THR A   8       1.269  -4.173  -1.451  1.00  0.00           H  
+ATOM    102  HB  THR A   8       1.334  -4.187   1.527  1.00  0.00           H  
+ATOM    103  HG1 THR A   8       3.759  -3.990   0.158  1.00  0.00           H  
+ATOM    104 HG21 THR A   8       1.575  -6.036  -0.564  1.00  0.00           H  
+ATOM    105 HG22 THR A   8       1.884  -6.336   1.147  1.00  0.00           H  
+ATOM    106 HG23 THR A   8       3.208  -5.868   0.081  1.00  0.00           H  
+ATOM    107  N   TRP A   9      -1.014  -4.864  -0.632  1.00  0.00           N  
+ATOM    108  CA  TRP A   9      -2.453  -5.058  -0.377  1.00  0.00           C  
+ATOM    109  C   TRP A   9      -2.656  -5.717   0.990  1.00  0.00           C  
+ATOM    110  O   TRP A   9      -3.517  -6.556   1.162  1.00  0.00           O  
+ATOM    111  CB  TRP A   9      -3.043  -5.945  -1.472  1.00  0.00           C  
+ATOM    112  CG  TRP A   9      -4.054  -5.163  -2.241  1.00  0.00           C  
+ATOM    113  CD1 TRP A   9      -4.281  -5.276  -3.568  1.00  0.00           C  
+ATOM    114  CD2 TRP A   9      -4.970  -4.148  -1.750  1.00  0.00           C  
+ATOM    115  NE1 TRP A   9      -5.292  -4.396  -3.922  1.00  0.00           N  
+ATOM    116  CE2 TRP A   9      -5.747  -3.679  -2.833  1.00  0.00           C  
+ATOM    117  CE3 TRP A   9      -5.200  -3.599  -0.479  1.00  0.00           C  
+ATOM    118  CZ2 TRP A   9      -6.723  -2.696  -2.660  1.00  0.00           C  
+ATOM    119  CZ3 TRP A   9      -6.179  -2.609  -0.299  1.00  0.00           C  
+ATOM    120  CH2 TRP A   9      -6.940  -2.158  -1.388  1.00  0.00           C  
+ATOM    121  H   TRP A   9      -0.514  -5.543  -1.118  1.00  0.00           H  
+ATOM    122  HA  TRP A   9      -2.936  -4.098  -0.395  1.00  0.00           H  
+ATOM    123  HB2 TRP A   9      -2.255  -6.270  -2.137  1.00  0.00           H  
+ATOM    124  HB3 TRP A   9      -3.516  -6.806  -1.023  1.00  0.00           H  
+ATOM    125  HD1 TRP A   9      -3.762  -5.943  -4.239  1.00  0.00           H  
+ATOM    126  HE1 TRP A   9      -5.652  -4.282  -4.827  1.00  0.00           H  
+ATOM    127  HE3 TRP A   9      -4.611  -3.941   0.364  1.00  0.00           H  
+ATOM    128  HZ2 TRP A   9      -7.306  -2.353  -3.502  1.00  0.00           H  
+ATOM    129  HZ3 TRP A   9      -6.349  -2.193   0.683  1.00  0.00           H  
+ATOM    130  HH2 TRP A   9      -7.692  -1.397  -1.244  1.00  0.00           H  
+ATOM    131  N   GLY A  10      -1.870  -5.345   1.962  1.00  0.00           N  
+ATOM    132  CA  GLY A  10      -2.020  -5.954   3.315  1.00  0.00           C  
+ATOM    133  C   GLY A  10      -1.022  -7.102   3.475  1.00  0.00           C  
+ATOM    134  O   GLY A  10      -0.340  -7.406   2.510  1.00  0.00           O  
+ATOM    135  OXT GLY A  10      -0.958  -7.658   4.558  1.00  0.00           O  
+ATOM    136  H   GLY A  10      -1.180  -4.668   1.804  1.00  0.00           H  
+ATOM    137  HA2 GLY A  10      -1.831  -5.203   4.069  1.00  0.00           H  
+ATOM    138  HA3 GLY A  10      -3.023  -6.335   3.429  1.00  0.00           H  
+CONECT    1    5    2    7    6                                       
+CONECT    2    3    9    1    8                                       
+CONECT    3   10    4    4    2                                       
+CONECT    4    3    3                                                 
+CONECT    5    1                                                      
+CONECT    6    1                                                      
+CONECT    7    1                                                      
+CONECT    8    2                                                      
+CONECT    9    2                                                      
+CONECT   10   11   22    3                                            
+CONECT   11   14   23   12   10                                       
+CONECT   12   11   13   13   31                                       
+CONECT   13   12   12                                                 
+CONECT   14   15   24   25   11                                       
+CONECT   15   16   16   17   14                                       
+CONECT   16   18   26   15   15                                       
+CONECT   17   19   19   15   27                                       
+CONECT   18   28   20   20   16                                       
+CONECT   19   20   29   17   17                                       
+CONECT   20   21   18   18   19                                       
+CONECT   21   30   20                                                 
+CONECT   22   10                                                      
+CONECT   23   11                                                      
+CONECT   24   14                                                      
+CONECT   25   14                                                      
+CONECT   26   16                                                      
+CONECT   27   17                                                      
+CONECT   28   18                                                      
+CONECT   29   19                                                      
+CONECT   30   21                                                      
+CONECT   31   12   39   32                                            
+CONECT   32   33   31   40   35                                       
+CONECT   33   34   34   43   32                                       
+CONECT   34   33   33                                                 
+CONECT   35   32   42   41   36                                       
+CONECT   36   35   37   37   38                                       
+CONECT   37   36   36                                                 
+CONECT   38   36                                                      
+CONECT   39   31                                                      
+CONECT   40   32                                                      
+CONECT   41   35                                                      
+CONECT   42   35                                                      
+CONECT   43   44   33   49                                            
+CONECT   44   50   47   45   43                                       
+CONECT   45   46   46   44   57                                       
+CONECT   46   45   45                                                 
+CONECT   47   52   51   44   48                                       
+CONECT   48   47   54   53   49                                       
+CONECT   49   43   48   56   55                                       
+CONECT   50   44                                                      
+CONECT   51   47                                                      
+CONECT   52   47                                                      
+CONECT   53   48                                                      
+CONECT   54   48                                                      
+CONECT   55   49                                                      
+CONECT   56   49                                                      
+CONECT   57   45   58   66                                            
+CONECT   58   67   57   59   61                                       
+CONECT   59   60   60   58   72                                       
+CONECT   60   59   59                                                 
+CONECT   61   58   62   69   68                                       
+CONECT   62   70   61   71   63                                       
+CONECT   63   62   65   65   64                                       
+CONECT   64   63                                                      
+CONECT   65   63   63                                                 
+CONECT   66   57                                                      
+CONECT   67   58                                                      
+CONECT   68   61                                                      
+CONECT   69   61                                                      
+CONECT   70   62                                                      
+CONECT   71   62                                                      
+CONECT   72   59   73   79                                            
+CONECT   73   74   80   72   76                                       
+CONECT   74   75   75   86   73                                       
+CONECT   75   74   74                                                 
+CONECT   76   73   78   81   77                                       
+CONECT   77   76   82                                                 
+CONECT   78   85   83   76   84                                       
+CONECT   79   72                                                      
+CONECT   80   73                                                      
+CONECT   81   76                                                      
+CONECT   82   77                                                      
+CONECT   83   78                                                      
+CONECT   84   78                                                      
+CONECT   85   78                                                      
+CONECT   86   87   90   74                                            
+CONECT   87   92   91   88   86                                       
+CONECT   88   89   89   87   93                                       
+CONECT   89   88   88                                                 
+CONECT   90   86                                                      
+CONECT   91   87                                                      
+CONECT   92   87                                                      
+CONECT   93   88   94  100                                            
+CONECT   94  101   93   95   97                                       
+CONECT   95  107   94   96   96                                       
+CONECT   96   95   95                                                 
+CONECT   97   94   99   98  102                                       
+CONECT   98  103   97                                                 
+CONECT   99  104  106   97  105                                       
+CONECT  100   93                                                      
+CONECT  101   94                                                      
+CONECT  102   97                                                      
+CONECT  103   98                                                      
+CONECT  104   99                                                      
+CONECT  105   99                                                      
+CONECT  106   99                                                      
+CONECT  107  121  108   95                                            
+CONECT  108  111  107  122  109                                       
+CONECT  109  108  110  110  131                                       
+CONECT  110  109  109                                                 
+CONECT  111  112  123  124  108                                       
+CONECT  112  113  113  114  111                                       
+CONECT  113  125  115  112  112                                       
+CONECT  114  116  116  112  117                                       
+CONECT  115  126  113  116                                            
+CONECT  116  115  118  114  114                                       
+CONECT  117  114  119  119  127                                       
+CONECT  118  128  116  120  120                                       
+CONECT  119  120  117  117  129                                       
+CONECT  120  118  118  130  119                                       
+CONECT  121  107                                                      
+CONECT  122  108                                                      
+CONECT  123  111                                                      
+CONECT  124  111                                                      
+CONECT  125  113                                                      
+CONECT  126  115                                                      
+CONECT  127  117                                                      
+CONECT  128  118                                                      
+CONECT  129  119                                                      
+CONECT  130  120                                                      
+CONECT  131  109  136  132                                            
+CONECT  132  131  138  133  137                                       
+CONECT  133  134  134  132  135                                       
+CONECT  134  133  133                                                 
+CONECT  135  133                                                      
+CONECT  136  131                                                      
+CONECT  137  132                                                      
+CONECT  138  132                                                      
+MASTER        0    0    0    0    0    0    0    0  138    0  138    0
+END

entangled-tps/data/chignolin/path.gro

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e1b886d2e29e11d4ac2080ca6cfb49deb4df2af352c9a94364a5c9b612b74a2c
+size 31686336

entangled-tps/data/chignolin/tica_model.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c96f96cc1a47e14babc588e432997b0d4877fa9980cc5f45a7c7788e49e1e38e
+size 86291

entangled-tps/data/chignolin/unfolded.pdb

@@ -0,0 +1,277 @@
+ATOM      1  N   GLY A   1       2.442   9.156  -5.701  1.00  0.00           N
+ATOM      2  CA  GLY A   1       3.003   9.402  -4.424  1.00  0.00           C
+ATOM      3  C   GLY A   1       4.122   8.405  -4.140  1.00  0.00           C
+ATOM      4  O   GLY A   1       4.722   7.912  -5.026  1.00  0.00           O
+ATOM      5  H   GLY A   1       2.094  10.047  -6.024  1.00  0.00           H
+ATOM      6  H2  GLY A   1       1.624   8.604  -5.484  1.00  0.00           H
+ATOM      7  H3  GLY A   1       3.106   8.676  -6.291  1.00  0.00           H
+ATOM      8  HA2 GLY A   1       3.561  10.337  -4.480  1.00  0.00           H
+ATOM      9  HA3 GLY A   1       2.216   9.620  -3.703  1.00  0.00           H
+ATOM     10  N   TYR A   2       4.448   8.113  -2.898  1.00  0.00           N
+ATOM     11  CA  TYR A   2       5.632   7.139  -2.581  1.00  0.00           C
+ATOM     12  C   TYR A   2       5.028   5.676  -2.559  1.00  0.00           C
+ATOM     13  O   TYR A   2       3.855   5.487  -2.235  1.00  0.00           O
+ATOM     14  CB  TYR A   2       6.143   7.396  -1.275  1.00  0.00           C
+ATOM     15  CG  TYR A   2       6.931   8.808  -1.152  1.00  0.00           C
+ATOM     16  CD1 TYR A   2       6.390   9.758  -0.314  1.00  0.00           C
+ATOM     17  CD2 TYR A   2       7.970   9.138  -2.016  1.00  0.00           C
+ATOM     18  CE1 TYR A   2       6.699  11.125  -0.591  1.00  0.00           C
+ATOM     19  CE2 TYR A   2       8.436  10.440  -2.164  1.00  0.00           C
+ATOM     20  CZ  TYR A   2       7.892  11.516  -1.319  1.00  0.00           C
+ATOM     21  OH  TYR A   2       8.569  12.633  -1.630  1.00  0.00           O
+ATOM     22  H   TYR A   2       3.893   8.462  -2.130  1.00  0.00           H
+ATOM     23  HA  TYR A   2       6.303   7.114  -3.439  1.00  0.00           H
+ATOM     24  HB2 TYR A   2       5.286   7.527  -0.615  1.00  0.00           H
+ATOM     25  HB3 TYR A   2       6.997   6.737  -1.118  1.00  0.00           H
+ATOM     26  HD1 TYR A   2       5.501   9.434   0.206  1.00  0.00           H
+ATOM     27  HD2 TYR A   2       8.186   8.304  -2.667  1.00  0.00           H
+ATOM     28  HE1 TYR A   2       6.364  11.941   0.032  1.00  0.00           H
+ATOM     29  HE2 TYR A   2       9.234  10.639  -2.864  1.00  0.00           H
+ATOM     30  HH  TYR A   2       8.061  13.381  -1.308  1.00  0.00           H
+ATOM     31  N   ASP A   3       5.913   4.639  -2.484  1.00  0.00           N
+ATOM     32  CA  ASP A   3       5.804   3.172  -2.156  1.00  0.00           C
+ATOM     33  C   ASP A   3       4.669   2.942  -1.007  1.00  0.00           C
+ATOM     34  O   ASP A   3       4.934   3.483   0.092  1.00  0.00           O
+ATOM     35  CB  ASP A   3       7.205   2.595  -1.827  1.00  0.00           C
+ATOM     36  CG  ASP A   3       7.311   1.068  -1.550  1.00  0.00           C
+ATOM     37  OD1 ASP A   3       6.499   0.321  -2.183  1.00  0.00           O
+ATOM     38  OD2 ASP A   3       8.002   0.635  -0.623  1.00  0.00           O
+ATOM     39  H   ASP A   3       6.853   5.005  -2.542  1.00  0.00           H
+ATOM     40  HA  ASP A   3       5.434   2.742  -3.087  1.00  0.00           H
+ATOM     41  HB2 ASP A   3       8.047   2.941  -2.427  1.00  0.00           H
+ATOM     42  HB3 ASP A   3       7.467   2.782  -0.786  1.00  0.00           H
+ATOM     43  N   PRO A   4       3.580   2.175  -1.326  1.00  0.00           N
+ATOM     44  CA  PRO A   4       2.414   1.706  -0.531  1.00  0.00           C
+ATOM     45  C   PRO A   4       2.852   0.500   0.294  1.00  0.00           C
+ATOM     46  O   PRO A   4       3.647  -0.381  -0.181  1.00  0.00           O
+ATOM     47  CB  PRO A   4       1.364   1.207  -1.442  1.00  0.00           C
+ATOM     48  CG  PRO A   4       1.546   2.002  -2.725  1.00  0.00           C
+ATOM     49  CD  PRO A   4       3.074   2.070  -2.671  1.00  0.00           C
+ATOM     50  HA  PRO A   4       2.103   2.610  -0.007  1.00  0.00           H
+ATOM     51  HB2 PRO A   4       1.480   0.158  -1.714  1.00  0.00           H
+ATOM     52  HB3 PRO A   4       0.320   1.258  -1.132  1.00  0.00           H
+ATOM     53  HG2 PRO A   4       1.220   1.520  -3.646  1.00  0.00           H
+ATOM     54  HG3 PRO A   4       1.216   3.039  -2.668  1.00  0.00           H
+ATOM     55  HD2 PRO A   4       3.372   1.126  -3.127  1.00  0.00           H
+ATOM     56  HD3 PRO A   4       3.536   2.825  -3.307  1.00  0.00           H
+ATOM     57  N   GLU A   5       2.373   0.465   1.518  1.00  0.00           N
+ATOM     58  CA  GLU A   5       2.721  -0.619   2.358  1.00  0.00           C
+ATOM     59  C   GLU A   5       1.492  -1.211   2.928  1.00  0.00           C
+ATOM     60  O   GLU A   5       0.595  -0.511   3.350  1.00  0.00           O
+ATOM     61  CB  GLU A   5       3.650  -0.105   3.468  1.00  0.00           C
+ATOM     62  CG  GLU A   5       4.893   0.774   3.091  1.00  0.00           C
+ATOM     63  CD  GLU A   5       5.354   1.571   4.471  1.00  0.00           C
+ATOM     64  OE1 GLU A   5       5.240   0.949   5.551  1.00  0.00           O
+ATOM     65  OE2 GLU A   5       5.911   2.733   4.424  1.00  0.00           O
+ATOM     66  H   GLU A   5       1.514   0.994   1.562  1.00  0.00           H
+ATOM     67  HA  GLU A   5       3.341  -1.273   1.744  1.00  0.00           H
+ATOM     68  HB2 GLU A   5       3.023   0.458   4.160  1.00  0.00           H
+ATOM     69  HB3 GLU A   5       3.839  -1.014   4.039  1.00  0.00           H
+ATOM     70  HG2 GLU A   5       5.786   0.311   2.669  1.00  0.00           H
+ATOM     71  HG3 GLU A   5       4.495   1.578   2.471  1.00  0.00           H
+ATOM     72  N   THR A   6       1.246  -2.477   2.792  1.00  0.00           N
+ATOM     73  CA  THR A   6      -0.108  -3.080   2.811  1.00  0.00           C
+ATOM     74  C   THR A   6      -1.347  -2.253   2.502  1.00  0.00           C
+ATOM     75  O   THR A   6      -2.124  -1.847   3.315  1.00  0.00           O
+ATOM     76  CB  THR A   6      -0.461  -3.643   4.177  1.00  0.00           C
+ATOM     77  OG1 THR A   6       0.846  -4.169   4.744  1.00  0.00           O
+ATOM     78  CG2 THR A   6      -1.433  -4.884   4.198  1.00  0.00           C
+ATOM     79  H   THR A   6       1.955  -2.902   2.212  1.00  0.00           H
+ATOM     80  HA  THR A   6      -0.164  -3.849   2.040  1.00  0.00           H
+ATOM     81  HB  THR A   6      -0.787  -2.796   4.782  1.00  0.00           H
+ATOM     82  HG1 THR A   6       1.512  -3.526   4.490  1.00  0.00           H
+ATOM     83 HG21 THR A   6      -1.698  -5.093   3.162  1.00  0.00           H
+ATOM     84 HG22 THR A   6      -2.395  -4.519   4.558  1.00  0.00           H
+ATOM     85 HG23 THR A   6      -0.936  -5.678   4.754  1.00  0.00           H
+ATOM     86  N   GLY A   7      -1.601  -2.024   1.238  1.00  0.00           N
+ATOM     87  CA  GLY A   7      -2.792  -1.493   0.548  1.00  0.00           C
+ATOM     88  C   GLY A   7      -3.911  -2.501   0.091  1.00  0.00           C
+ATOM     89  O   GLY A   7      -4.433  -2.291  -0.978  1.00  0.00           O
+ATOM     90  H   GLY A   7      -0.824  -2.331   0.670  1.00  0.00           H
+ATOM     91  HA2 GLY A   7      -3.303  -0.868   1.280  1.00  0.00           H
+ATOM     92  HA3 GLY A   7      -2.504  -0.902  -0.321  1.00  0.00           H
+ATOM     93  N   THR A   8      -4.046  -3.643   0.769  1.00  0.00           N
+ATOM     94  CA  THR A   8      -4.908  -4.678   0.348  1.00  0.00           C
+ATOM     95  C   THR A   8      -5.821  -5.309   1.496  1.00  0.00           C
+ATOM     96  O   THR A   8      -5.236  -6.022   2.379  1.00  0.00           O
+ATOM     97  CB  THR A   8      -4.418  -5.877  -0.652  1.00  0.00           C
+ATOM     98  OG1 THR A   8      -3.720  -5.332  -1.784  1.00  0.00           O
+ATOM     99  CG2 THR A   8      -5.612  -6.624  -1.264  1.00  0.00           C
+ATOM    100  H   THR A   8      -3.292  -3.834   1.414  1.00  0.00           H
+ATOM    101  HA  THR A   8      -5.725  -4.105  -0.090  1.00  0.00           H
+ATOM    102  HB  THR A   8      -3.633  -6.476  -0.190  1.00  0.00           H
+ATOM    103  HG1 THR A   8      -4.217  -4.512  -1.746  1.00  0.00           H
+ATOM    104 HG21 THR A   8      -6.346  -6.979  -0.540  1.00  0.00           H
+ATOM    105 HG22 THR A   8      -5.163  -7.511  -1.710  1.00  0.00           H
+ATOM    106 HG23 THR A   8      -6.432  -6.015  -1.644  1.00  0.00           H
+ATOM    107  N   TRP A   9      -7.189  -5.332   1.418  1.00  0.00           N
+ATOM    108  CA  TRP A   9      -8.243  -6.319   1.819  1.00  0.00           C
+ATOM    109  C   TRP A   9      -9.168  -6.736   0.607  1.00  0.00           C
+ATOM    110  O   TRP A   9      -9.248  -6.174  -0.549  1.00  0.00           O
+ATOM    111  CB  TRP A   9      -8.800  -5.866   3.214  1.00  0.00           C
+ATOM    112  CG  TRP A   9      -9.614  -6.753   4.010  1.00  0.00           C
+ATOM    113  CD1 TRP A   9     -10.894  -6.733   4.104  1.00  0.00           C
+ATOM    114  CD2 TRP A   9      -9.137  -7.780   4.952  1.00  0.00           C
+ATOM    115  NE1 TRP A   9     -11.363  -7.476   5.149  1.00  0.00           N
+ATOM    116  CE2 TRP A   9     -10.269  -8.144   5.743  1.00  0.00           C
+ATOM    117  CE3 TRP A   9      -7.868  -8.369   5.264  1.00  0.00           C
+ATOM    118  CZ2 TRP A   9     -10.191  -8.963   6.750  1.00  0.00           C
+ATOM    119  CZ3 TRP A   9      -7.818  -8.924   6.540  1.00  0.00           C
+ATOM    120  CH2 TRP A   9      -8.921  -9.323   7.252  1.00  0.00           C
+ATOM    121  H   TRP A   9      -7.746  -4.623   0.964  1.00  0.00           H
+ATOM    122  HA  TRP A   9      -7.757  -7.233   2.159  1.00  0.00           H
+ATOM    123  HB2 TRP A   9      -8.098  -5.440   3.931  1.00  0.00           H
+ATOM    124  HB3 TRP A   9      -9.466  -5.023   3.031  1.00  0.00           H
+ATOM    125  HD1 TRP A   9     -11.430  -6.001   3.517  1.00  0.00           H
+ATOM    126  HE1 TRP A   9     -12.339  -7.480   5.408  1.00  0.00           H
+ATOM    127  HE3 TRP A   9      -6.940  -8.301   4.716  1.00  0.00           H
+ATOM    128  HZ2 TRP A   9     -11.127  -9.178   7.243  1.00  0.00           H
+ATOM    129  HZ3 TRP A   9      -6.824  -9.260   6.797  1.00  0.00           H
+ATOM    130  HH2 TRP A   9      -8.986  -9.733   8.249  1.00  0.00           H
+ATOM    131  N   GLY A  10      -9.841  -7.874   0.709  1.00  0.00           N
+ATOM    132  CA  GLY A  10     -10.490  -8.642  -0.346  1.00  0.00           C
+ATOM    133  C   GLY A  10      -9.646  -9.737  -0.865  1.00  0.00           C
+ATOM    134  O   GLY A  10      -8.824  -9.742  -1.894  1.00  0.00           O
+ATOM    135  OXT GLY A  10      -9.783 -10.762  -0.231  1.00  0.00           O
+ATOM    136  H   GLY A  10      -9.683  -8.434   1.535  1.00  0.00           H
+ATOM    137  HA2 GLY A  10     -11.470  -9.051  -0.099  1.00  0.00           H
+ATOM    138  HA3 GLY A  10     -10.788  -7.967  -1.149  1.00  0.00           H
+CONECT    1    5    2    7    6                                       
+CONECT    2    3    9    1    8                                       
+CONECT    3   10    4    4    2                                       
+CONECT    4    3    3                                                 
+CONECT    5    1                                                      
+CONECT    6    1                                                      
+CONECT    7    1                                                      
+CONECT    8    2                                                      
+CONECT    9    2                                                      
+CONECT   10   11   22    3                                            
+CONECT   11   14   23   12   10                                       
+CONECT   12   11   13   13   31                                       
+CONECT   13   12   12                                                 
+CONECT   14   15   24   25   11                                       
+CONECT   15   16   16   17   14                                       
+CONECT   16   18   26   15   15                                       
+CONECT   17   19   19   15   27                                       
+CONECT   18   28   20   20   16                                       
+CONECT   19   20   29   17   17                                       
+CONECT   20   21   18   18   19                                       
+CONECT   21   30   20                                                 
+CONECT   22   10                                                      
+CONECT   23   11                                                      
+CONECT   24   14                                                      
+CONECT   25   14                                                      
+CONECT   26   16                                                      
+CONECT   27   17                                                      
+CONECT   28   18                                                      
+CONECT   29   19                                                      
+CONECT   30   21                                                      
+CONECT   31   12   39   32                                            
+CONECT   32   33   31   40   35                                       
+CONECT   33   34   34   43   32                                       
+CONECT   34   33   33                                                 
+CONECT   35   32   42   41   36                                       
+CONECT   36   35   37   37   38                                       
+CONECT   37   36   36                                                 
+CONECT   38   36                                                      
+CONECT   39   31                                                      
+CONECT   40   32                                                      
+CONECT   41   35                                                      
+CONECT   42   35                                                      
+CONECT   43   44   33   49                                            
+CONECT   44   50   47   45   43                                       
+CONECT   45   46   46   44   57                                       
+CONECT   46   45   45                                                 
+CONECT   47   52   51   44   48                                       
+CONECT   48   47   54   53   49                                       
+CONECT   49   43   48   56   55                                       
+CONECT   50   44                                                      
+CONECT   51   47                                                      
+CONECT   52   47                                                      
+CONECT   53   48                                                      
+CONECT   54   48                                                      
+CONECT   55   49                                                      
+CONECT   56   49                                                      
+CONECT   57   45   58   66                                            
+CONECT   58   67   57   59   61                                       
+CONECT   59   60   60   58   72                                       
+CONECT   60   59   59                                                 
+CONECT   61   58   62   69   68                                       
+CONECT   62   70   61   71   63                                       
+CONECT   63   62   65   65   64                                       
+CONECT   64   63                                                      
+CONECT   65   63   63                                                 
+CONECT   66   57                                                      
+CONECT   67   58                                                      
+CONECT   68   61                                                      
+CONECT   69   61                                                      
+CONECT   70   62                                                      
+CONECT   71   62                                                      
+CONECT   72   59   73   79                                            
+CONECT   73   74   80   72   76                                       
+CONECT   74   75   75   86   73                                       
+CONECT   75   74   74                                                 
+CONECT   76   73   78   81   77                                       
+CONECT   77   76   82                                                 
+CONECT   78   85   83   76   84                                       
+CONECT   79   72                                                      
+CONECT   80   73                                                      
+CONECT   81   76                                                      
+CONECT   82   77                                                      
+CONECT   83   78                                                      
+CONECT   84   78                                                      
+CONECT   85   78                                                      
+CONECT   86   87   90   74                                            
+CONECT   87   92   91   88   86                                       
+CONECT   88   89   89   87   93                                       
+CONECT   89   88   88                                                 
+CONECT   90   86                                                      
+CONECT   91   87                                                      
+CONECT   92   87                                                      
+CONECT   93   88   94  100                                            
+CONECT   94  101   93   95   97                                       
+CONECT   95  107   94   96   96                                       
+CONECT   96   95   95                                                 
+CONECT   97   94   99   98  102                                       
+CONECT   98  103   97                                                 
+CONECT   99  104  106   97  105                                       
+CONECT  100   93                                                      
+CONECT  101   94                                                      
+CONECT  102   97                                                      
+CONECT  103   98                                                      
+CONECT  104   99                                                      
+CONECT  105   99                                                      
+CONECT  106   99                                                      
+CONECT  107  121  108   95                                            
+CONECT  108  111  107  122  109                                       
+CONECT  109  108  110  110  131                                       
+CONECT  110  109  109                                                 
+CONECT  111  112  123  124  108                                       
+CONECT  112  113  113  114  111                                       
+CONECT  113  125  115  112  112                                       
+CONECT  114  116  116  112  117                                       
+CONECT  115  126  113  116                                            
+CONECT  116  115  118  114  114                                       
+CONECT  117  114  119  119  127                                       
+CONECT  118  128  116  120  120                                       
+CONECT  119  120  117  117  129                                       
+CONECT  120  118  118  130  119                                       
+CONECT  121  107                                                      
+CONECT  122  108                                                      
+CONECT  123  111                                                      
+CONECT  124  111                                                      
+CONECT  125  113                                                      
+CONECT  126  115                                                      
+CONECT  127  117                                                      
+CONECT  128  118                                                      
+CONECT  129  119                                                      
+CONECT  130  120                                                      
+CONECT  131  109  136  132                                            
+CONECT  132  131  138  133  137                                       
+CONECT  133  134  134  132  135                                       
+CONECT  134  133  133                                                 
+CONECT  135  133                                                      
+CONECT  136  131                                                      
+CONECT  137  132                                                      
+CONECT  138  132                                                      
+END