I am getting a significant difference between the R-factors written by phenix.refine and phenix.model_vs_data. 1. Phenix.refine phenix.refine "in.pdb" "Fobs.mtz" "refinement.input.xray_data.labels=FP SIGFP" "refinement.input.xray_data.high_resolution=2.50" "fix_rotamers=True" "ordered_solvent=True" "strategy=tls+individual_sites+individual_adp" Final R-work = 0.1829, R-free = 0.2141 2. Phenix.model_vs_data phenix.model_vs_data out.pdb Fobs.mtz f_obs_label="FP" r_free_flags_label="FreeR_flag" high_resolution=2.50 comprehensive=true r_work(re-computed) : 0.1808 r_free(re-computed) : 0.2099 How can I reproduce the phenix.refine R-factors in phenix.model_vs_data? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992