[phenixbb] Gap between R and Rfree

[Pavel Afonine]

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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>>> phenixbb at phenix-online.org
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>>>
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