[phenixbb] Rfree % calculation

Pavel Afonine pafonine at lbl.gov
Thu Jan 22 08:41:44 PST 2015


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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