Compare these two lines from phenix.refine:
REMARK 3 NUMBER OF REFLECTIONS : 46001
REMARK 3 FREE R VALUE TEST SET COUNT : 2339
with those from refmac, ostensibly using the same data and start pdb:
REMARK 3 NUMBER OF REFLECTIONS : 43672
REMARK 3 FREE R VALUE TEST SET COUNT : 2339
I know there are 46011 reflections with |F|>0 in the files I used.
phenix.refine removes 10 of these as outliers. The 46001 remaining
reported in REMARK 3 *include* the test set.
With REFMAC, 43672+2339=46011 so it appears that Refmac reports just the
*working* set count in that first line, excluding the test set.
Is this is a bug with one program or the other, or a bug in the PDB
definition of REMARK 3 ?
http://www.wwpdb.org/documentation/format23/remark3.html
This appears to be a source of inconsistency.
phenix.refine 1.6-289
refmac5 5.4.0077 (I'm apparently a Luddite)
Phil Jeffrey
Princeton
