[phenixbb] Inconsistent R-factors in PDB file

[Schubert, Carsten [PRDUS]]

Hi,

Not sure if this has been asked before but recently I noticed phenix
seems to report inconsistent R-values after each refinement. The final
values reported in the screen output 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 a
deposition it matters a bit more. So which values should I report for a
paper?

Cheers,

	Carsten


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