Hi all, 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. Also, I read in an old post in ccp4 ( http://www.dl.ac.uk/list-archive-public/ccp4bb/2006-07/msg00205.html) which gave some suggestions about how to fix the Ranmanchandran outliers “you could re-solve your protein with arp/warp if resolution is high enough, or rebuild the side chains with gui-side if not; refine that structure and, if the residue is no longer an outlier after refinement, adopt that rotamer for your structure. But I think it might be faster to manually cycle through a library of rotamers (and try both pep-flip), select all that appear possible, and refine starting from there”. I have a couple of questions about the suggestions above: 1. For my resolution 3.2 Å, which strategy should I try first? 2. “Resolve the structure with arp/warp”, is this to say rebuild the structure automatically again? 3. “Rebuild the side chains with gui-side”, in which program and how could this be done? 4. “manually cycle through a library of rotamers (and try both pep-flip), select all that appear possible, and refine starting from there”. I am wondering using which program and how could this be done? Thank you so much! Best, Wei
