Re: [phenixbb] Gap between R and Rfree

25 Feb 2010

      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  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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