[phenixbb] Phenix.refine bonds/angles rmsd

guanrj at foxmail.com guanrj at foxmail.com
Wed Apr 14 07:09:56 PDT 2010

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?


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 ******************** 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 ************************************************************************

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!
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