[phenixbb] Gap between R and Rfree

Maia Cherney chern at ualberta.ca
Thu Feb 25 10:38:31 PST 2010

My suggestion is try a different refinement program.


Phil Jeffrey wrote:
> More information would be very helpful for giving detailed 
> suggestions, however:
> 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
> Princeton
> 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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