Hi Pavel Thanks for your suggestion. I have another question: I am refining another 3.3 A resolution structure. In coot I manually adjusted the model to have >95% residues in preferred region in ramanchandran plot, but after refinement in Phenix only <80% residues in the preferred region and a lot more in the outlier region. This was wen I used the default refinement parameters "phenix.refine mtz_file pdb_file". R and R_free are 0.22/0.27 in this case. Then when I used "phenix.refine mtz_file pdb_file wxc_scale=0.1 wxu_scale=0.3", I can get better results in terms of ramanchandran plot (say, ~92% in preferred region, and a little more in the outlier). R and R_free factors are 0.25/0.30. I guess at low resolution (like in my case, 3.3 A) I have to give more weights to geometry restrains. Did I do it in the right way, or did I missing anything? Thanks Rongjin Guan = = = = = = = = On 2010-04-13 16:42:21 You wrote = = = = = = = = Hi Rongjin, when I use phenix.refine to refine my structure, the rmsd's of bonds and angles are pretty large. My data is 2.3 A resolution. REMARK REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.2838 r_free = 0.2789 bonds = 0.029 angles = 2.002 REMARK Final: r_work = 0.2407 r_free = 0.2466 bonds = 0.029 angles = 2.002 REMARK ************************************************************************ REMARK really (just wondering)? What I would be really worry is the difference between Rfree and Rwork, which apparently is terribly small, indicating that there is something wrong with either free-R flags or refinement strategy. I tried many options but none worked so far. Here are the options that I tried: phenix.refine mtz_file pdb_file strategy=tls tls_group_selections.params wxc_scale=0.3 wxu_scale=0.8 phenix.refine mtz_file pdb_file strategy=tls tls_group_selections.params fix_wxc=0.3 fix_wxu=0.8 phenix.refine mtz_file pdb_file strategy=tls tls_group_selections.params fix_wxc=0.3 fix_wxu=0.8 optimize_wxc=false optimize_wxu=false These gave the same refinement results. Any suggestions? It's not surprising, because in all refinements above you did not refine the coordinates at all. The keyword "strategy=tls" means you refined B-factors only (more precisely, you did constrained anisotropic refinement, called TLS refinement). And therefore using wxc_scale or fix_wxc or optimize_wxc would not make any difference. Also, optimize_wxc is set to False by default, so you don't need to explicitly say it. I would run it like this: phenix.refine mtz_file pdb_file strategy=tls+individual_adp+individual_sites tls_group_selections.params optimize_wxc=true and hope that this fixes the "problem". Let me know if you have any questions! Pavel.