[phenixbb] Gap between R and Rfree
Francis E Reyes
Francis.Reyes at Colorado.EDU
Thu Feb 25 09:45:49 PST 2010
Pavel
What phenix utility produces such information?
Thx
FR
On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:
> Hi Young-Jin,
>
> the distribution of R-factors for all structures in PDB refined at
> resolutions between 2.4 and 2.6 A is following:
>
> Histogram of Rwork for all model in PDB at resolution 2.40-2.60:
> 0.115 - 0.141 : 5
> 0.141 - 0.168 : 69
> 0.168 - 0.194 : 414
> 0.194 - 0.220 : 955 <<<<< your structure
> 0.220 - 0.246 : 695
> 0.246 - 0.273 : 153
> 0.273 - 0.299 : 25
> 0.299 - 0.325 : 5
> 0.325 - 0.352 : 0
> 0.352 - 0.378 : 1
> Histogram of Rfree for all model in PDB at resolution 2.40-2.60:
> 0.146 - 0.178 : 3
> 0.178 - 0.210 : 41
> 0.210 - 0.242 : 404
> 0.242 - 0.274 : 1104
> 0.274 - 0.305 : 653 <<<<< your structure
> 0.305 - 0.337 : 108
> 0.337 - 0.369 : 8
> 0.369 - 0.401 : 0
> 0.401 - 0.433 : 0
> 0.433 - 0.465 : 1
> Histogram of Rfree-Rwork for all model in PDB at resolution 2.40-2.60:
> 0.002 - 0.012 : 28
> 0.012 - 0.022 : 83
> 0.022 - 0.031 : 232
> 0.031 - 0.041 : 430
> 0.041 - 0.051 : 458
> 0.051 - 0.061 : 493
> 0.061 - 0.071 : 298
> 0.071 - 0.080 : 186
> 0.080 - 0.090 : 85 <<<<< your structure
> 0.090 - 0.100 : 29
>
> which I interpret as your Rwork is most likely good as well as
> Rfree, but the gap Rfree-Rwork is too large meaning possible
> overfitting.
>
> A few tips:
> - if you have NCS - use it in refinement;
> - optimize refinement target weights: a) automatically:
> "optimize_wxc=true optimize_wxu=true", or b) manually using
> wxc_scale and wxu_scale parameters;
> - make sure you use the latest PHENIX version.
>
> Let me now if you have any questions.
>
> Pavel.
>
>
> On 2/25/10 9:17 AM, 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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