[phenixbb] fix Ramachandran outliers
pafonine at lbl.gov
Tue Jul 30 10:28:36 PDT 2013
> Thank you guys so much for the suggestions! I don't know why I still
> have rotamer outliers after real-space refinement. I am wondering what
> might go wrong and what I should check in this case?
which Phenix version you use? Anyway, sounds like you don't have rotamer
outliers as statistics below indicates.
> At the same time, I fixed the Ramanchandran outliers and rotamer
> outliers in Coot, and did another refinement with default setting +
> NCS restraints + secondary structure restraints + optimize X-ray/
> stereochemistry + optimize X-ray/ ADP. Are these refinement settings
> look reasonable to you?
> Below are the results:
> R-work: 0.2542, R-free: 0.2857, Angles: 1, Bonds: 0.003.
> Ramachandran outliers: 0.4% (Goal: <0.2%), Ramachandran favored: 92.6%
> (Goal: >98%).
> Rotamer outliers: 0 % (Goal: 1%), c-beta outliers: 0 (Goal: 0)
> clashscore: 6.92, overall score: 1.85.
Looks ok to me.
> But, when I opened the results in coot, do Ramanchandran plot, and I
> couldn't see any Ramanchandran outliers.
This is because Coot and Phenix use slightly different Ramachandran plot
libraries. I guess Paul Emsley or/and Jeff can offer more comments on this.
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