On Thu, Apr 19, 2012 at 7:37 AM, Mario Sanches
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 minimizer. 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 values. -Nat