[phenixbb] fix Ramachandran outliers

Wei Shi wei.shi118 at gmail.com
Sun Jul 28 12:44:55 PDT 2013

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 a previous post that “all outliers could be first fixed
manually in Coot (also applying real-space refinement with Coot's
Ramachandran restraints turned on), as the default potential is very tight
and can pull residues the wrong way if they're starting from a very bad

I am wondering whether any of you have done this before in coot, and can
you please tell me specifically how this is done. Thank you so much!


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