[phenixbb] Gap between R and Rfree
Simon Kolstoe
s.kolstoe at ucl.ac.uk
Thu Feb 25 14:01:28 PST 2010
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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