Hi, I want to use phenix to refine a model right after autobuild with the following script: phenix.refine xray_data.file_name=exptl_fobs_phases_freeR_flags.mtz overall_best-090903a.pdb strategy=rigid_body+individual_sites simulated_annealing=true simulated_annealing.start_temperature=8000 sites.rigid_body="chain A" sites.rigid_body="chain B" However, the program says " F-obs: exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP If previously used R-free flags are available run this command again with the name of the file containing the original flags as an additional input. If the structure was never refined before, or if the original R-free flags are unrecoverable, run this command again with the additional definition: refinement.input.xray_data.r_free_flags.generate=True when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my data, while the refinement program does not recognize it? label #valid %valid min max type H 35619 100.00% 0.00 22.00 H: index h,k,l K 35619 100.00% 0.00 45.00 H: index h,k,l L 35619 100.00% -33.00 33.00 H: index h,k,l FP 35619 100.00% 0.00 114.22 F: amplitude SIGFP 35619 100.00% 0.15 6.13 Q: standard deviation PHIM 35619 100.00% 0.00 0.00 P: phase angle in degrees FOMM 35619 100.00% 0.00 0.00 W: weight (of some sort) FreeR_flag 35619 100.00% 0.00 1.00 I: integer FC 35619 100.00% 0.00 0.00 F: amplitude