  We present an analysis of the pion-nucleon $\sigma$-term, $\sigma_{\pi N}$,
using six ensembles with 2+1+1-flavor highly improved staggered quark action
generated by the MILC collaboration. The most serious systematic effect in
lattice calculations of nucleon correlation functions is the contribution of
excited states. We estimate these using chiral perturbation theory ($\chi$PT),
and show that the leading contribution to the isoscalar scalar charge comes
from N$\pi$ and N$\pi\pi$ states. Therefore, we carry out two analyses of
lattice data to remove excited-state contamination, the standard one and a new
one including N$\pi$ and N$\pi\pi$ states. We find that the standard analysis
gives $\sigma_{\pi N} = 41.9(4.9)$ MeV, consistent with previous lattice
calculations, while our preferred $\chi$PT-motivated analysis gives
$\sigma_{\pi N} = 59.6(7.4)$ MeV, which is consistent with phenomenological
values obtained using $\pi$N scattering data. Our data on one physical pion
mass ensemble was crucial for exposing this difference, therefore, calculations
on additional physical mass ensembles are needed to confirm our result and
resolve the tension between lattice QCD and phenomenology.
