I am tring to refine the predicted structure from alphafold and SWISS-MODEL database. Since the protocol I followed said I need to eliminate the steric clash and do refinement in predicted structure first (and then docking or some other analysis).
So I just relaxed protein in torsion space with constraints. And here is the code I used:
relax.mpi.linuxgccrelease -s 5B0U.pdb -relax: constrain_relax_to_start_coords -ramp_constraints false -relax: coord_constrain_sidechains -nstruct 20 -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false
But when I used Structure Assessment from Swiss-model to evaluate relax result( I choose the lowest one) , I found all of the protein's clash score were significantly increased (17.6 to 207 or 0.46 to 174), and the overall MolProbity Score were also increased (ideal case is as low as possible)
So I am confused about these results, and do not know if these proteins become better or not after relaxing by rosetta. Or just trust rosetta results and follow the protocol?
Thanks in advance for any responses on this question,