Hello 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 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? Thanks Rongjin Guan