I mentioned previously phenix.refine tosses your weak data if IMEAN, SIGIMEAN are chosen during refinement.
I'm wondering if this omission of weak Fobs from the Fobs-Fcalc difference map explains why the difference maps out of refmac seem to be more helpful in showing where to move atoms. D. Crowfoot et al. in The Chemistry of Penicillin (1949) explain why this might be so, and Stout & Jenson elaborate the argument. Briefly, the calculated phase will be closest to the phase of the vector difference Fcalc - Fobs when |Fcalc| > |Fobs|. I leave it to the reader to try calculating some maps with and without the weak Fobs in phenix.refine or refmac, and perhaps making some deliberate rotamer errors, to see if using the complete data with weak Fobs helps.
