Hello Wei, I have a refined structure with phenix. >
FYI and as a reminder: there is Phenix mailing list for Phenix-specific questions. > The resolution=3.2 Å. After refinement, the R-work=0.2186, R-free=0.2864, > Bonds=0.010, Angles=1.515. > Large Rfree-Rwork gap indicates overfitting, which in turn makes me think that refinement strategy you use is not optimal for the data and model you have. If you send me files off list I may be able to suggest a better option. > Rotamer outliers: 14.5%, c-beta outliers: 2 > This suggests me that you may not be using a recent version of the program, since recent versions fix problems like this in real space and apply rotamer-specific and cbeta restraints during refinement, and these restraints are updated dynamically. > To fix the Ramanchandran outliers, in coot, by changing the phi-psi of the > outliers, I could manage to move most of them to the allowed positions. > But, after another refinement in phenix, those outliers come back. > This is a scenario when you may want to apply Ramachandran restraints locally to residues that are notorious outliers. Steps to do this are: - first, fix Ramachandran outliers manually, - then, running subsequent refinement include these residues into Ramachandran restraints. However, I think you may even not need to do this if you use optimal refinement strategy (see above): the fact that you get notorious outliers may be a result of not using correct refinement strategy. Good luck! Pavel
