[phenixbb] Gap between R and Rfree

Young-Jin Cho yjcho at brandeis.edu
Thu Feb 25 09:41:34 PST 2010

Thanks for your suggestions, Phill.
When I did Ramachandran analysis, it shows 96.60% in preferred region and 2.62% in allowed regions, and 0.79% is in outlier. Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls option. it didn't help much.
Now I am trying to scale down.

Thanks again.


0.  Use Molprobity or the Validation tools in Coot to look at your 
structure and see what errors you can fix.
1.  What is your geometry like ?  Try reducing wxc_scale (try 
wxc_scale=0.5) and see what happens.
2.  What is the variation of B-factors across bonds ?  Try reducing 
wxu_scale - perhaps wxu_scale=0.5 or less.
2a.  phenix.refine is autocratic about wxu_scale if you're using TLS so 
setting it yourself does not help.
3.  Since R-free of 0.298 is a little high for a 2.5 Angstrom structure, 
you should carefully check your model.  Perhaps you have a high 
proportion of disordered structure, which can cause this.  If you feel 
that your model is correct, you could explore using TLS on your model. 
Potential TLS groups can be found using the TLSMD server at: 
http://skuld.bmsc.washington.edu/~tlsmd/  although the results should 
always be filtered through a common-sense definition of domain/group 
boundaries (e.g. don't break in the middle of helices unless there's a 
good reason to).

Phil Jeffrey

Young-Jin Cho wrote:
> Hi everyone,
> I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on).
> Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful.
> Thanks in advance,
> Young-Jin
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Postdoctoral Fellow, Kern Lab
Biochemistry Department/HHMI
Brandeis University

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