[phenixbb] fix Ramachandran outliers

Pavel Afonine pafonine at lbl.gov
Tue Jul 30 10:28:36 PDT 2013

Hi Wei,

> 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.


More information about the phenixbb mailing list