[phenixbb] Inconsistent R-factors in PDB file
Pavel Afonine
pafonine at lbl.gov
Mon May 30 13:07:11 PDT 2011
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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