Hi Yarrow, thanks for sending log files. Completeness reported in log files reflects the content of input MTZ data files: *32.log:* (...) F-obs: (...) Miller array info: (...)/reflectionsFreeR_1.38A.mtz:F_New(+),SIGF_New(+),F_New(-),SIGF_New(-),systematic_absences_eliminated Observation type: xray.amplitude Type of data: double, size=325598 Type of sigmas: double, size=325598 Number of Miller indices: 325598 Anomalous flag: True Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 (...) and *35.log:* (...) I-obs: (...) Miller array info: (...)/reflectionsFandIFreeR_1.38A.mtz:IMEAN_New,SIGIMEAN_New,systematic_absences_eliminated Observation type: xray.intensity Type of data: double, size=181940 Type of sigmas: double, size=181940 Number of Miller indices: 181940 Anomalous flag: False Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 (...) The numbers above are reported before anything else is done, that is they reflect exactly what's in input MTZ files. Somehow you managed to loose ~10% of data when converting Iobs into Fobs. How did you do this conversion? In theory this is possible since French&Wilson Iobs->Fobs conversion may result on some number of reflections lost. Note, when phenix.refine does IMEAN->Fobs conversion (35.log file) this does not result in ~10% loss. So based on looking at log files I can say it's not phenix.refine that manipulated your data or reported it wrong. You lost reflections at previous steps. Pavel On 12/4/12 4:57 PM, Yarrow Madrona wrote:

Hi,

Here are the log files for refinement you asked for.

35.log is refined with Intensities. The MTZ file has a slightly different name but it is the same MTZ. One had Intensities taken out of it because I didn't think I needed them any longer.

32.log is refined with structure factors. Intensities were removed.

Thanks for your help!

-Yarrow