[phenixbb] FreeR set reduced by half in twin crystal refinement?
lauren at gate.sinica.edu.tw
Thu Oct 8 01:27:59 PDT 2009
Thanks for all your reply, really helpful
>My first guess is that the R-free set generated in CCP4 is not set to
follow twin laws, so you have work and free reflections associated by
twinning. However, I would expect PHENIX >to check this.
>As for the reduced size, that probably comes from the way the twinned test
set is calculated. Maybe it is a bug. Are you using anomalous data?
>What is the PHENIX version?
>- you have at least n% of free flags, but not more then 2000+epsilon
>- it follows any possible twin law (not user specified, it follows symmetry
of the lattice)
After I change the setting "xray_data.r_free_flags.max_free ", and set it up
xray_data.r_free_flags.fraction=0.05, the results look normal.
Final: r_work = 0.1782 r_free = 0.2285 bonds = 0.007 angles = 1.186
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.1807
REMARK 3 R VALUE (WORKING SET) : 0.1782
REMARK 3 FREE R VALUE : 0.2285
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.07
REMARK 3 FREE R VALUE TEST SET COUNT : 2776
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