Re: [phenixbb] fix Ramachandran outliers

If real-space refinement was part of refinement then I wonder why you still have rotamer outliers. Their amount should be way smaller (close to 0 at this resolution, if not precisely zero!), so there must be something else that isn't quite right, which is hard to tell without looking at the files. Pavel On 7/28/13 2:33 PM, Wei Shi wrote:

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 mailto:[email protected]> wrote:

On Sun, Jul 28, 2013 at 12:44 PM, Wei Shi mailto:[email protected]> 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 _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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