[phenixbb] Geometry Restraints

Mario Sanches mariosan at gmail.com
Thu Apr 19 05:37:35 PDT 2012

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

Is there a known procedure to deal with this? I feel that my geometry
weighing term is too loose but I don't know exactly how to tighten it other
than decreasing the wxc_scale parameter. I have gone and manually corrected
bad positions before but given the low resolution nature of the structure
the clashes tend to be reestablished during refinement.

Thank you in advance for your help,

Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
M5G 1X5
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