[phenixbb] Gap between R and Rfree

Young-Jin Cho yjcho at brandeis.edu
Thu Feb 25 11:45:04 PST 2010

Thanks everyone.
First, I checked my data and showed almost no anisotropy.
Second, I tried both refmac and phenix, had the similar results.
Third, ncs may be the key... I re-processed hkl and cut the resolution and did ncs=true. It first generated error message and suggested to put distance limit upto 3. Then now the gap between R and Rfree is reasonable (.2834 and .3361 without substrate and water). 
However I tried my previous pdb that has everything with old mtz file, Final R-work = 0.2389, R-free = 0.3158. In this case, I had to expand my limit upto 6.  

I still need to look more or do further refine from newly generated mtz file though, (sorry that's why I was late for responding.... I wanted to confirm it). Anyway, seemingly setting up 'ncs' as Pavel mentioned is most possible answer to my case.

Thanks again.


----- Original Message -----
From: "Kendall Nettles" <knettles at scripps.edu>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Thursday, February 25, 2010 1:35:10 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Gap between R and Rfree

Did you check your data


On Feb 25, 2010, at 12:43 PM, "Young-Jin Cho" <yjcho at brandeis.edu>  

> 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.
> Young-Jin
> 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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