[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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>   



More information about the phenixbb mailing list