[phenixbb] statistics for highest shell in phenix.refine

Pavel Afonine PAfonine at lbl.gov
Wed Sep 5 15:03:14 PDT 2007


Hi Michael,

phenix.refine reports the Rwork- and R-free factor statistics in bins 
(as well as completeness, fom, phase error estimates, number of 
reflections, etc). Look in you .log file for a table like this:

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          
Targets        |
|number     range              work test   work   test        
work        test|
|  1: 24.6802 -  3.7756 0.97   1800  135 0.2554 0.3150      6.0946      
6.2202|
|  2:  3.7756 -  2.9985 0.99   1845  140 0.2466 0.2738      6.1306      
6.4268|
|  3:  2.9985 -  2.6200 0.99   1819  156 0.2738 0.3065      5.9144      
6.1387|
|  4:  2.6200 -  2.3806 0.99   1820  143 0.2662 0.3266      5.7197      
5.8192|
|  5:  2.3806 -  2.2101 0.99   1813  138 0.2515 0.3138      5.5753      
5.6897|
|  6:  2.2101 -  2.0799 0.99   1844  135 0.2518 0.2708      5.4776      
5.5673|
|  7:  2.0799 -  1.9758 0.99   1818  140 0.2512 0.3325      5.3948       
5.728|
|  8:  1.9758 -  1.8898 0.99   1806  144 0.2652 0.3208      5.3259      
5.5097|
|  9:  1.8898 -  1.8171 0.98   1833  137 0.2450 0.2865      5.1955      
5.2526|
| 10:  1.8171 -  1.7544 0.98   1765  165 0.2660 0.3250      5.0805      
5.2769|
| 11:  1.7544 -  1.6995 0.99   1872  128 0.2538 0.3600      4.9928      
5.2402|
| 12:  1.6995 -  1.6510 0.98   1770  152 0.2550 0.2989      4.8696      
5.0337|
| 13:  1.6510 -  1.6075 0.96   1798  153 0.2609 0.2944      4.7976      
5.0056|
| 14:  1.6075 -  1.5683 0.95   1708  137 0.2554 0.3106      4.7096      
4.9238|
| 15:  1.5683 -  1.5327 0.90   1686  145 0.2450 0.3115      4.6753      
4.8214|
| 16:  1.5327 -  1.5000 0.86   1590  110 0.2452 0.3547       4.609      
4.8343|
|-----------------------------------------------------------------------------|

In this particular example above the numbers you are interested in are 
located in the line # 16: Rwork=0.2452 and Rfree=0.3547.

A few things to keep in mind:

1) phenix.refine prints this table several times: before, during and 
after refinement, so make sure you're looking the latest one (printed 
just before refinement finishes);

2) If you're using the latest version of phenix.refine (from PHENIX or 
CCI Apps), then the PDB file header contains similar statistics in bins 
so you don't need to look at long .log file.

Please let me know if you have any questions.
Pavel.



michael hothorn wrote:
> Dear all,
>
> For the crystallographic table in my manuscript, can I define a highest
> shell in phenix.refine and have it output the refinement statistics for
> this range? If not, how can I calculate the highest shell statistics
> using the same parameters as used for the overall refinment?
>
> Thanks
> Michael 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb



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