Dear Phil,
Can we turn the argument on its head ?
well, it depends what you call "head" -:)
Short version:
phenix.refine throws out 2896 reflections of 48895, including 11% of the data in the outermost shell, compared to using TRUNCATE to prep my data. Using the common data subset the structure has a decreased R-free of 0.8% if you refine against the truncate=yes PDB file with the common subset of data.
0.8% at a 24% R-free (24.0 vs 24.8) is pretty significant IMHO.
You cannot compare the R-factors that were computed using different sets of reflections. Therefore the above comparison is not valid, obviously. Same applies to your "Longer version". Let's compare apples with apples. Comparing R-factors in this case does not tell that one refinement is better or worse than the other one. It just doesn't tell anything because the R-factor is not a good measure when you deal with two different datasets (datasets containing different amount of reflections). Pavel.