On Thu, Apr 19, 2012 at 5:37 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.
I'm guessing Pavel has already sorted this out - but an expert shouldn't be required to yield appropriate geometry/chemistry! This sort of problem has been discussed previously: http://phenix-online.org/pipermail/phenixbb/2011-November/017906.html http://dx.doi.org/10.1107/S0907444911039060 although that high of a clashscore could arise from something else? Regards, Tim