[phenixbb] fix Ramachandran outliers

[Pavel Afonine]

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