There seems to be a large discrepancy between the likelihood-based coordinate error estimate depending on whether the intensities or structure factor magnitudes are used, which doesn't make any sense to me. If I do: % phenix.refine rebuild.pdb data_withI.mtz phenix.refine picks up Imean and SigImean from the MTZ and refines the structure xray_data { file_name = "data_withI.mtz" labels = "IMEAN,SIGIMEAN" r_free_flags { file_name = "data_withI.mtz" label = "FreeR_flag" test_flag_value = 0 } then I get: | maximum likelihood estimate for coordinate error: 1.39 A But if I create an MTZ file without the intensities by using CAD on the original file, and use the same coordinate file: % phenix.refine rebuild.pdb data_withoutI.mtz phenix.refine picks up the structure factors instead: xray_data { file_name = "data_withoutI.mtz" labels = "F,SIGF" r_free_flags { file_name = "data_withoutI.mtz" label = "FreeR_flag" test_flag_value = 0 } } then this seems to be the right ballpark for a 1.75 Angstrom structure.... | maximum likelihood estimate for coordinate error: 0.28 A Similar R-factors, but there is a factor of 10 difference in the scale reported here: I's: r_work= 0.2266 r_free= 0.2570 ksol= 0.41 Bsol= 50.00 scale= 0.097 F's: r_work= 0.2221 r_free= 0.2557 ksol= 0.41 Bsol= 50.00 scale= 0.965 Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.6 User: phil Cheers, Phil Jeffrey Princeton