Hi all

Thanks for all your reply, really helpful

Joe wrote,

>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?

No anomalous

>What is the PHENIX version?

Peter wrote,

>- you have at least n% of free flags, but not more then 2000+epsilon

>(typically)

>- 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 to 5000.
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

Best Regards

Lauren