[phenixbb] R/Rfree from phenix.autobuild
Pavel Afonine
pafonine at lbl.gov
Thu Nov 27 09:53:51 PST 2008
Hi Graeme,
the difference between Rwork and Rfree depends on resolution. Here is
some R-factor statistics for all PDB structures refined at resolution
range between 1.55A and 1.65A:
Distribution of R-work at resolution 1.55-1.65
Resolution range Number of structures
9.90 - 11.86: 6
11.86 - 13.82: 28
13.82 - 15.78: 185
15.78 - 17.74: 415
17.74 - 19.70: 562
19.70 - 21.66: 358
21.66 - 23.62: 144
23.62 - 25.58: 27
25.58 - 27.54: 8
27.54 - 29.50: 2
Distribution of R-free 1.55-1.65
Resolution range Number of structures
14.00 - 15.93: 11
15.93 - 17.86: 73
17.86 - 19.79: 293
19.79 - 21.72: 490
21.72 - 23.65: 458
23.65 - 25.58: 244
25.58 - 27.51: 110
27.51 - 29.44: 39
29.44 - 31.37: 11
31.37 - 33.30: 6
Distribution of R-work-Rfree 1.55-1.65
Resolution range Number of structures
0.10 - 1.23: 69
1.23 - 2.36: 426
2.36 - 3.49: 562
3.49 - 4.62: 401
4.62 - 5.75: 163
5.75 - 6.88: 67
6.88 - 8.01: 31
8.01 - 9.14: 11
9.14 - 10.27: 3
10.27 - 11.40: 2
1% difference in your case is suspiciously small indeed. Although
Autobuld combines model building with refinement using phenix.refine,
its main purpose to build the structure and not produce the best refined
possible one. After Autobuld you may want to do some more refinement
customized to your particular case (resolution, etc...). At 1.6A you may
want to try:
- refining anisotropic ADP;
- if refinement of anisotropic ADP is prohibitive (Rfree and Rfree-Rwork
go too high), try TLS instead;
- simply do more refinement macro-cycles to achieve full convergence (by
default phenix.refine does 3 macro-cycles), say try 5, for example;
- optimize weights using automatic options (use "optimize_wxc=true
optimize_wxu=true" - this may take a while to finish), or try a few
different values manually (wxc_scale=..., wxu_scale=...).
Please let us know if you have any other questions!
Pavel.
On 11/27/2008 8:54 AM, Graeme Winter wrote:
> Hi Folks,
>
> Quick question about R/Rfree from phenix - I ran the autobuild and it
> kindly built pretty much all of the visible residues, and it gave me
> the following output:
>
> SOLUTION CYCLE R RFREE BUILT PLACED
> 1 1 0.22 0.23 169 169
> 2 2 0.21 0.23 170 170
> 3 4 0.22 0.23 170 170
>
> Now, I'm not one to complain about good results, but I did feel that
> the Rfree looked a little close to the R factor - usually I would
> expect a difference of maybe 4-5%. Is there a reason for this that I
> am missing? The model seemed to fit very nicely, closely corresponded
> to the PDB entry and the waters were pretty good. There is no NCS (one
> copy in the ASU) and the phases are from SeMet mad data from Autosol.
>
> Resolution is ~1.6A, if that is any help.
>
> Just noticed this and thought it was interesting. I am used to
> Arp/wArp for automated tracing, which typically gives a bigger
> difference...
>
> Many thanks,
>
> Graeme
> _______________________________________________
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> phenixbb at phenix-online.org
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>
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