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Hi Graeme,<br>
<br>
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:<br>
<br>
<font face="Courier New, Courier, monospace">Distribution of R-work at
resolution 1.55-1.65<br>
Resolution range Number of structures<br>
9.90 - 11.86: 6<br>
11.86 - 13.82: 28<br>
13.82 - 15.78: 185<br>
15.78 - 17.74: 415<br>
17.74 - 19.70: 562<br>
19.70 - 21.66: 358<br>
21.66 - 23.62: 144<br>
23.62 - 25.58: 27<br>
25.58 - 27.54: 8<br>
27.54 - 29.50: 2<br>
<br>
Distribution of R-free 1.55-1.65<br>
</font><font face="Courier New, Courier, monospace"> Resolution range
Number of structures</font><br>
<font face="Courier New, Courier, monospace"> 14.00 - 15.93: 11<br>
15.93 - 17.86: 73<br>
17.86 - 19.79: 293<br>
19.79 - 21.72: 490<br>
21.72 - 23.65: 458<br>
23.65 - 25.58: 244<br>
25.58 - 27.51: 110<br>
27.51 - 29.44: 39<br>
29.44 - 31.37: 11<br>
31.37 - 33.30: 6<br>
<br>
Distribution of R-work-Rfree 1.55-1.65<br>
</font><font face="Courier New, Courier, monospace"> Resolution range
Number of structures</font><br>
<font face="Courier New, Courier, monospace"> 0.10 - 1.23: 69<br>
1.23 - 2.36: 426<br>
2.36 - 3.49: 562<br>
3.49 - 4.62: 401<br>
4.62 - 5.75: 163<br>
5.75 - 6.88: 67<br>
6.88 - 8.01: 31<br>
8.01 - 9.14: 11<br>
9.14 - 10.27: 3<br>
10.27 - 11.40: 2<br>
</font><br>
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:<br>
<br>
- refining anisotropic ADP;<br>
- if refinement of anisotropic ADP is prohibitive (Rfree and
Rfree-Rwork go too high), try TLS instead;<br>
- simply do more refinement macro-cycles to achieve full convergence
(by default phenix.refine does 3 macro-cycles), say try 5, for example;<br>
- 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=...).<br>
<br>
Please let us know if you have any other questions!<br>
<br>
Pavel.<br>
<br>
<br>
On 11/27/2008 8:54 AM, Graeme Winter wrote:
<blockquote
cite="mid:23e06a570811270854x5fbcbf37jb1cdc8fe39df559b@mail.gmail.com"
type="cite">
<pre wrap="">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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