[phenixbb] Gap between R and Rfree
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 25 11:39:45 PST 2010
Hi Francis,
in PHENIX GUI: "Validation" -> "PDB Statistics Overview"
or:
in PHENIX GUI: "Validation" -> "POLYGON"
The underlying idea is published here:
Crystallographic model quality at a glance. L. Urzhumtseva, P. V.
Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009)
I can add a command line version if anyone is interested.
Pavel.
On 2/25/10 9:45 AM, Francis E Reyes wrote:
> 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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>>>
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