Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.
In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.
Chain identifier: A
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: What type of B-factor?
WHAT IF does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. TLS seems not mentioned in the header of the PDB
file. But anyway, if WHAT IF complains about your B-factors, and you think
that they are OK, then check for TLS related B-factor problems first.
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
103 ARG ( 482-) A
118 TYR ( 497-) A
11 PHE ( 386-) A 46 PHE ( 421-) A 96 PHE ( 475-) A
155 GLU ( 534-) A
RMS Z-score for bond lengths: 0.568
RMS-deviation in bond distances: 0.014
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.
Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.
If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.
Unit Cell deformation matrix
| 0.995331 0.000136 -0.000070| | 0.000136 0.995777 0.000567| | -0.000070 0.000567 0.996960|Proposed new scale matrix
| 0.020147 -0.000003 0.000001| | -0.000002 0.014128 -0.000008| | 0.000000 -0.000008 0.013500|With corresponding cell
A = 49.635 B = 70.783 C = 74.074 Alpha= 89.935 Beta= 90.004 Gamma= 89.984
The CRYST1 cell dimensions
A = 49.867 B = 71.081 C = 74.300 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 7.238
Error: Nomenclature error(s)
Checking for a hand-check. WHAT IF has over the course of this session
already corrected the handedness of atoms in several residues. These were
administrative corrections. These residues are listed here.
103 ARG ( 482-) A 155 GLU ( 534-) A
Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.
Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
145 GLU ( 524-) A C -6.3 -9.23 -0.03 The average deviation= 1.370
79 LEU ( 454-) A 5.51 155 GLU ( 534-) A 4.12 78 LEU ( 453-) A 4.07
These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.
7 TYR ( 382-) A -3.0 119 PRO ( 498-) A -3.0 96 PHE ( 475-) A -2.4 64 THR ( 439-) A -2.3 9 LYS ( 384-) A -2.1 60 GLY ( 435-) A -2.1
Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.
5 GLY ( 380-) A Poor phi/psi 7 TYR ( 382-) A Poor phi/psi 64 THR ( 439-) A Poor phi/psi 96 PHE ( 475-) A Poor phi/psi 98 SER ( 477-) A Poor phi/psi 118 TYR ( 497-) A PRO omega poor 145 GLU ( 524-) A PRO omega poor chi-1/chi-2 correlation Z-score : 0.183
For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.
A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!
4 ILE ( 379-) A 0 8 SER ( 383-) A 0 9 LYS ( 384-) A 0 12 LEU ( 387-) A 0 17 ASP ( 392-) A 0 20 HIS ( 395-) A 0 36 THR ( 411-) A 0 40 SER ( 415-) A 0 51 CYS ( 426-) A 0 53 TYR ( 428-) A 0 62 ILE ( 437-) A 0 63 LYS ( 438-) A 0 64 THR ( 439-) A 0 68 LEU ( 443-) A 0 69 PRO ( 444-) A 0 79 LEU ( 454-) A 0 84 ALA ( 459-) A 0 85 PRO ( 460-) A 0 86 LYS ( 465-) A 0 87 ARG ( 466-) A 0 94 CSO ( 473-) A 0 95 GLU ( 474-) A 0 96 PHE ( 475-) A 0 97 SER ( 476-) A 0 99 GLU ( 478-) A 0And so on for a total of 80 lines.
Standard deviation of omega values : 2.248
Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level. See:
Who checks the checkers? Four validation tools applied to eight atomic
resolution structures [REF]
82 PRO ( 457-) A 0.46 HIGH
28 PRO ( 403-) A 100.2 envelop C-beta (108 degrees)
The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.
The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
1 MET ( 376-) A CE <-> 24 LYS ( 399-) A CE 0.41 2.79 INTRA 1 MET ( 376-) A CE <-> 24 LYS ( 399-) A CD 0.30 2.90 INTRA 20 HIS ( 395-) A ND1 <-> 106 ARG ( 485-) A NH2 0.24 2.76 INTRA 100 ARG ( 479-) A NE <-> 174 HOH ( 126 ) A O 0.19 2.51 INTRA 111 ARG ( 490-) A NH1 <-> 174 HOH ( 137 ) A O 0.13 2.57 INTRA 63 LYS ( 438-) A NZ <-> 174 HOH ( 148 ) A O 0.06 2.64 INTRA 63 LYS ( 438-) A NZ <-> 174 HOH ( 46 ) A O 0.04 2.66 INTRA 20 HIS ( 395-) A NE2 <-> 99 GLU ( 478-) A OE1 0.04 2.66 INTRA 56 GLU ( 431-) A OE2 <-> 100 ARG ( 479-) A NH1 0.03 2.67 INTRA BL 98 SER ( 477-) A OG <-> 174 HOH ( 106 ) A O 0.02 2.38 INTRA 93 HIS ( 472-) A NE2 <-> 174 HOH ( 7 ) A O 0.01 2.69 INTRA BL
Chain identifier: A
Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing environment.
The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.
118 TYR ( 497-) A -8.07 169 ARG ( 548-) A -7.03 14 GLN ( 389-) A -5.46
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
169 ARG ( 548-) A 171 - TRP 550- ( A) -5.17
Chain identifier: A
Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate unusual packing.
Chain identifier: A
Water, ion, and hydrogenbond related checks
Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a hydrogen
atom that is not involved in a hydrogen bond in the optimized hydrogen bond
Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.
Waters are not listed by this option.
11 PHE ( 386-) A N 46 PHE ( 421-) A N 93 HIS ( 472-) A ND1 98 SER ( 477-) A N 100 ARG ( 479-) A NH1 101 GLY ( 480-) A N 133 TYR ( 512-) A N
112 ASP ( 491-) A H-bonding suggests Asn; but Alt-Rotamer
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.265 2nd generation packing quality : -0.954 Ramachandran plot appearance : -0.431 chi-1/chi-2 rotamer normality : 0.183 Backbone conformation : -0.998
Bond lengths : 0.568 (tight) Bond angles : 0.768 Omega angle restraints : 0.409 (tight) Side chain planarity : 0.637 (tight) Improper dihedral distribution : 1.144 B-factor distribution : 0.647 Inside/Outside distribution : 1.032
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.
Resolution found in PDB file : 1.70
Structure Z-scores, positive is better than average:
1st generation packing quality : -1.1 2nd generation packing quality : -1.0 Ramachandran plot appearance : -0.8 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -1.3
Bond lengths : 0.568 (tight) Bond angles : 0.768 Omega angle restraints : 0.409 (tight) Side chain planarity : 0.637 (tight) Improper dihedral distribution : 1.144 B-factor distribution : 0.647 Inside/Outside distribution : 1.032 ==============
WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform Bond lengths and angles, protein residues R.Engh and R.Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392--400 (1991). Bond lengths and angles, DNA/RNA G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman, New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D52, 57--64 (1996). DSSP W.Kabsch and C.Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features Biopolymers 22, 2577--2637 (1983). Hydrogen bond networks R.W.W.Hooft, C.Sander and G.Vriend, Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures PROTEINS, 26, 363--376 (1996). Matthews' Coefficient B.W.Matthews Solvent content of Protein Crystals J. Mol. Biol. 33, 491--497 (1968). Protein side chain planarity R.W.W. Hooft, C. Sander and G. Vriend, Verification of protein structures: side-chain planarity J. Appl. Cryst. 29, 714--716 (1996). Puckering parameters D.Cremer and J.A.Pople, A general definition of ring puckering coordinates J. Am. Chem. Soc. 97, 1354--1358 (1975). Quality Control G.Vriend and C.Sander, Quality control of protein models: directional atomic contact analysis, J. Appl. Cryst. 26, 47--60 (1993). Ramachandran plot G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations J. Mol. Biol. 7, 95--99 (1963). Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994). Ion Checks I.D.Brown and K.K.Wu, Empirical Parameters for Calculating Cation-Oxygen Bond Valences Acta Cryst. B32, 1957--1959 (1975). M.Nayal and E.Di Cera, Valence Screening of Water in Protein Crystals Reveals Potential Na+ Binding Sites J.Mol.Biol. 256 228--234 (1996). P.Mueller, S.Koepke and G.M.Sheldrick, Is the bond-valence method able to identify metal atoms in protein structures? Acta Cryst. D 59 32--37 (2003). Checking checks K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. Who checks the checkers J.Mol.Biol. (1998) 276,417-436.