To help you draft a detailed paper, I have structured this template based on the most common scenario for such a file:
Report on the elimination of outliers in the Ramachandran phi/psi distributions. proteinFixed.rar
Filling missing coordinates using Modeller or Rosetta. To help you draft a detailed paper, I
In computational biology, protein structures often require "fixing"—the process of adding missing atoms, correcting non-standard residues, or optimizing hydrogen bond networks. correcting non-standard residues
Brief steepest-descent minimization using the AMBER or CHARMM force fields to remove atomic overlaps.
Use of tools like PDB2PQR to assign protonation states at pH 7.0.