[phenixbb] Geometry Restraints

Pavel Afonine pafonine at lbl.gov
Thu Apr 19 05:42:24 PDT 2012

Hi Mario,

are you using the latest Phenix? If not, please update your version of 
Phenix and try again:


If this doesn't help, please send me the data and model (offlist) and I 
will have a look to see what's  going on.


On 4/19/12 5:37 AM, Mario Sanches 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.
> 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
> Canada
> M5G 1X5
> http://ca.linkedin.com/in/mariosanches
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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