Hello, default setting is 10% with max 2000 reflections. As Georg said, 0=Work and 1=Test (free). phenix.refine tries its best to figure out what are "work" and "free" flags, as different programs have different conventions. Unless you changed the default, I think you get more than 2000 flags because Fobs+ and Fobs- are counted as separate reflections (2 reflections), while each one of the two must have the same flag (for example, if Fobs+ is "1" then Fobs- must be "1" too). Pavel On 1/21/15 1:31 PM, Tarek DawoD wrote:
Dear ALL
when you start you refinment in phenix with ***.sca file, fraction of reflection in test set will be created. under *options *(bottom) in phenix refine, you could see that fraction of reflection in test set is 0.1 which means 10 % by looking to the PDB header for completely different structures (below) you will find different percentage but always FREE R VALUE TEST SET COUNT is around 3800. so it always take the same 3800 count regardless the number of reflections.
when you look in generated mtz file after the refinment, you see under R-free-flags(+) and R-free-flags(-) either 0 or 1. what does 0 or 1 mean?
thank you in advance for explaination.
TKDawoD
---------------------------------------------------------------------------------------------------- REMARK 3 NUMBER OF REFLECTIONS : 47312 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 24389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1673 REMARK 3 R VALUE (WORKING SET) : 0.1636 REMARK 3 FREE R VALUE : 0.2084 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.21 REMARK 3 FREE R VALUE TEST SET COUNT : 3882 ------------------------------------------------------------------------------------------------------ REMARK 3 NUMBER OF REFLECTIONS : 107005 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 56251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1457 REMARK 3 R VALUE (WORKING SET) : 0.15.34 REMARK 3 FREE R VALUE : 0.1997 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.51 REMARK 3 FREE R VALUE TEST SET COUNT : 3809 ----------------------------------------------------------------------------------------------------- NUMBER OF REFLECTIONS : 48150 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1507 REMARK 3 R VALUE (WORKING SET) : 0.1470 REMARK 3 FREE R VALUE : 0.1918 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.98 REMARK 3 FREE R VALUE TEST SET COUNT : 3841
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