Hi Rongjin,
when I use phenix.refine to refinemy structure, the rmsd's ofbonds 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 optionsthat I tried: phenix.refine mtz_filepdb_file strategy=tls tls_group_selections.paramswxc_scale=0.3 wxu_scale=0.8 phenix.refine mtz_filepdb_file strategy=tls tls_group_selections.paramsfix_wxc=0.3 fix_wxu=0.8 phenix.refine mtz_filepdb_file strategy=tls tls_group_selections.paramsfix_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.