Re: [phenixbb] fix Ramachandran outliers

Hi Dr Echols, Thank you for the suggestions. I ran the refinement again with default settings + Rigid body+ Simulated annealing (Cartesian) + Optimize X-ray/stereochemistry weight. And the statistics improved! See below: R-work=0.2348, R-free=0.2855, Bonds=0.003, Angles=0.919. Ramachandran outliers: 2.5%, Ramachandran favored: 88.1%. Rotamer outliers: 10%, c-beta outliers: 0 clashscore: 9.06, overall score: 2.84 Now, I am wondering whether there is any suggestion about what to try and check next to further refine the structure. Thank you so much! Best, Wei On Sun, Jul 28, 2013 at 4:00 PM, Nathaniel Echols wrote:

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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

On Sun, Jul 28, 2013 at 12:44 PM, Wei Shi wrote: the

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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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb