Hi Pavel,
4) Also, clashes related concerns may be a result of inoptimal weight between Xray target and restrains. Although one can play with the weight adjusting scales manually by trying different values of "wxc_scale" parameter ("wxu_scale" is analog for b-factors refinement) the new version of phenix.refine has an automatic procedure for finding the best weight (here "the best" means the weight that leads to the lowest Rfree) (Carsten's suggestion). To use this option:
% phenix.refine model.pdb data.mtz your_parameters.par optimize_wxc=true
Wouldn't it be better to try and get the highest Free Log Likelihood Gain (LLG) rather than the lowest Rfree? I would worry that trying to optimise Rfree rather than LLG or even a free Rxpct (a-la BUSTER) would be less stable/reliable. Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549