On Sun, Jul 28, 2013 at 12:44 PM, Wei Shi
I have a refined structure with phenix. The resolution=3.2 Å. After refinement, the R-work=0.2186, R-free=0.2864, Bonds=0.010, Angles=1.515.
Ramachandran outliers: 4.8%, Ramachandran favored: 80.8%.
Rotamer outliers: 14.5%, c-beta outliers: 2
clashscore: 16.28, overall score: 3.32
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.
I am wondering whether any of you have any suggestions for me on how to fix these outliers.
Turn on X-ray/stereochemistry weight optimization (for non-GUI users, optimize_xyz_weight=True). That usually fixes the problem. -Nat