[phenixbb] fix Ramachandran outliers

Wei Shi wei.shi118 at gmail.com
Tue Jul 30 10:15:25 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?

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.
But, when I opened the results in coot, do Ramanchandran plot, and I
couldn't see any Ramanchandran outliers.

Let me know any comments or suggestions about what to do or check next.
Thank you so much!

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