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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