[phenixbb] Inconsistent R-factors in PDB file

[Pavel Afonine]

Hi Carsten,

they have to match exactly, if they don't then there is something wrong 
somewhere...

I just did a few refinement runs and I can't reproduce this. What is the 
command that results in this inconsistency between R-factors?

Pavel.

On 5/30/11 11:07 AM, Schubert, Carsten [PRDUS] wrote:
>
> Hi,
>
> Not sure if this has been asked before but recently I noticed phenix 
> seems to report inconsistent R-values after each 
> refinement.Thefinalvalues reported in thescreenoutput after refinement 
> match the values reported in the'Quick Facts'section, but are not 
> matched by the values in the PDB deposition section. Attached is an 
> example:
>
> ...
>
> REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS 
> *******************
>
> REMARK Start: r_work = 0.1907 r_free = 0.2151 bonds = 0.004 angles = 0.727
>
> REMARK Final: r_work =*0.1838*r_free =*0.2141*bonds = 0.005 angles = 0.832
>
> REMARK 
> ************************************************************************
>
> ...
>
> REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP.
>
> REMARK   3
>
> REMARK   3 REFINEMENT.
>
> REMARK   3   PROGRAM     : PHENIX (phenix.refine: 1.7.1_743)
>
> REMARK   3   AUTHORS     : Adams,Afonine,Chen,Davis,Echols,Gopal,
>
> REMARK   3               : 
> Grosse-Kunstleve,Headd,Hung,Immormino,Ioerger,McCoy,
>
> REMARK   3               : 
> McKee,Moriarty,Pai,Read,Richardson,Richardson,Romo,
>
> REMARK   3               : 
> Sacchettini,Sauter,Smith,Storoni,Terwilliger,Zwart
>
> REMARK   3
>
> REMARK   3  REFINEMENT TARGET : ML
>
> REMARK   3
>
> REMARK   3  DATA USED IN REFINEMENT.
>
> REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.950
>
> REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 37.113
>
> REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.33
>
> REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.21
>
> REMARK   3   NUMBER OF REFLECTIONS             : 29410
>
> REMARK   3
>
> REMARK   3  FIT TO DATA USED IN REFINEMENT.
>
> REMARK   3   R VALUE     (WORKING + TEST SET) : 0.1894
>
> REMARK   3   R VALUE            (WORKING SET) :*0.1877*
>
> REMARK   3   FREE R VALUE                     :*0.2122*
>
> REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 6.74
>
> REMARK   3   FREE R VALUE TEST SET COUNT      : 1982
>
> For regular work I really don't care as long as the values are 
> consistent and tell me if the refinement reached convergence, but for 
> adeposition it matters a bit more. So which values should I reportfor 
> a paper?
>
> Cheers,
>
> Carsten
>
>
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