[phenixbb] Geometry Restraints

Nathaniel Echols nechols at lbl.gov
Thu Apr 19 05:48:18 PDT 2012

On Thu, Apr 19, 2012 at 7:37 AM, Mario Sanches <mariosan at gmail.com> wrote:
> I am refining a low resolution structure (2.9A) using phenix.refine. As I
> continue the refinement  Rwork/Rfree are dropping but my  geometry
> statistics in general are very bad. My clashscore is getting worst and the
> RMS(angle) is really high. I have tried to play with the "wxc_scale"
>  parameter and also ran phenix selecting the "Optimize X-ray/ADP weight"
> option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of
> ~190.

Did you mean to type "Optimize X-ray/Stereochemistry weight" instead?
That is the option you want to use in these situations; it usually
results in much better geometry, with two caveats:

1) If the input geometry is already poor, this may result in a poor
initial guess for the weight, and the optimization will not sample the
right range.

2) Severe clashes are hard to fix automatically - the structure needs
to be repacked to fix them, which is beyond the power of our

One tip: always run real-space refinement in Coot when rebuilding your
model.  Getting the input geometry as good as possible seems to help
phenix.refine (or any other refinement program) converge on acceptable


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