[phenixbb] Rfree % calculation

Tarek DawoD tkdawod at yahoo.com
Wed Jan 21 13:31:06 PST 2015


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) : 0.1673REMARK   3   R VALUE            (WORKING SET) : 0.1636REMARK   3   FREE R VALUE                     : 0.2084REMARK   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) : 0.1457REMARK   3   R VALUE            (WORKING SET) : 0.15.34REMARK   3   FREE R VALUE                     : 0.1997REMARK   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) : 0.1507REMARK   3   R VALUE            (WORKING SET) : 0.1470REMARK   3   FREE R VALUE                     : 0.1918REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 7.98  REMARK   3   FREE R VALUE TEST SET COUNT      : 3841     
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