[phenixbb] Gap between R and Rfree

Thu Feb 25 17:49:40 PST 2010

Hi Simon,

the next available PHENIX nightly build will have this command:

phenix.r_factor_statistics

This will output a plain text histograms for Rwork, Rfree and 
Rfree-Rwork. For example:

***
phenix.r_factor_statistics 2.5 left_offset=0.2 right_offset=0.2 n_bins=5
Command used:

phenix.r_factor_statistics 2.500 left_offset=0.200 right_offset=0.200 
n_bins=5

Histogram of Rwork for models in PDB at resolution 2.30-2.70 A:
     0.115 - 0.168      : 149
     0.168 - 0.220      : 2998
     0.220 - 0.273      : 1879
     0.273 - 0.325      : 67
     0.325 - 0.378      : 2
Histogram of Rfree for models in PDB at resolution 2.30-2.70 A:
     0.146 - 0.210      : 116
     0.210 - 0.274      : 3288
     0.274 - 0.337      : 1664
     0.337 - 0.401      : 26
     0.401 - 0.465      : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.30-2.70 A:
     0.001 - 0.021      : 233
     0.021 - 0.041      : 1412
     0.041 - 0.060      : 2180
     0.060 - 0.080      : 1045
     0.080 - 0.100      : 225
Number of structures considered: 5095
***

and running it without arguments will take all structures.

Pavel.

On 2/25/10 2:01 PM, Simon Kolstoe wrote:
> oh yes please Pavel (command line polygon/statistics overview) - could 
> the output be a pdf or ps rather than just starting up the GUI?
>
> Simon
>
>
>
> On 25 Feb 2010, at 19:39, Pavel Afonine wrote:
>
>> 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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