[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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