[phenixbb] fix Ramachandran outliers

[Nathaniel Echols]

On Sun, Jul 28, 2013 at 12:44 PM, Wei Shi <wei.shi118 at gmail.com> wrote:
> 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.

Turn on X-ray/stereochemistry weight optimization (for non-GUI users,
optimize_xyz_weight=True).  That usually fixes the problem.

-Nat