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 &quot;wxc_scale&quot;  parameter and also ran phenix selecting the &quot;Optimize X-ray/ADP weight&quot; option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of ~190. <div>
<br></div><div>Is there a known procedure to deal with this? I feel that my geometry weighing term is too loose but I don&#39;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. </div>
<div><br></div><div>Thank you in advance for your help,<br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>
Toronto - Ontario<br>Canada<br>M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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