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Hi Rongjin,<br>
<blockquote cite="mid:201004131728171257643@foxmail.com" type="cite"><font
face="Verdana" size="2">
<div>when I use phenix.refine to refine my structure, the rmsd's
of bonds and angles are </div>
<div>pretty large. My data is 2.3 A resolution. </div>
<div> </div>
<div>REMARK<br>
REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS
*******************<br>
REMARK Start: r_work = 0.2838 r_free = 0.2789 bonds = 0.029 angles =
2.002<br>
REMARK Final: r_work = 0.2407 r_free = 0.2466 bonds = 0.029 angles =
2.002<br>
REMARK
************************************************************************<br>
REMARK<br>
</div>
</font></blockquote>
<br>
really (just wondering)? <br>
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.<br>
<br>
<blockquote cite="mid:201004131728171257643@foxmail.com" type="cite"><font
face="Verdana" size="2">
<div>I tried many options but none worked so far. Here are the
options that I tried:</div>
<div> </div>
<div>phenix.refine mtz_file pdb_file strategy=tls
tls_group_selections.params wxc_scale=0.3 wxu_scale=0.8</div>
<div> </div>
<div>phenix.refine mtz_file pdb_file strategy=tls
tls_group_selections.params fix_wxc=0.3 fix_wxu=0.8 </div>
<div> </div>
<div>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</div>
<div> </div>
<div>These gave the same refinement results. Any suggestions?</div>
</font></blockquote>
<br>
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.<br>
<br>
I would run it like this:<br>
<br>
phenix.refine mtz_file pdb_file
strategy=tls+individual_adp+individual_sites
tls_group_selections.params optimize_wxc=true<br>
<br>
and hope that this fixes the "problem".<br>
<br>
Let me know if you have any questions!<br>
Pavel.<br>
<br>
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