[phenixbb] Gap between R and Rfree
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 25 09:43:47 PST 2010
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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