Inconsistent R-factors in PDB file
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
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
-
Pavel Afonine -
Schubert, Carsten [PRDUS]