Before revision:  bound refinement and forcefield-based energy minimization (EM)  . By comparing several metrics on conformation evaluation between our results and the PDB deposits, including RMSD, TMscore, MPscore, secondary structures and Ramachandran Plot, we conclude that our method is consistent with the popular used methods.
After revision:  bound refinement and forcefield-based energy minimization (EM) and water refinement . By comparing several metrics on conformation evaluation between our results and the PDB deposits, including RMSD, TMscore, MPscore, secondary structures and Ramachandran Plot, we conclude that our method is consistent with the popular used methods.