Hi Serah, You are right that the coefficients that you want for a difference map are not present in the overall_best_refine_map_coeffs.mtz file. The coefficients in that file (labelled FP PHIM) are the same as 2FOFCWT PH2FOFCWT from the refinement output, but there are no difference map coefficients. I will change this. In the meantime, I would do this after the end of autobuild: phenix.refine AutoBuild_run_1_/overall_best.pdb \ AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz and then you will have your map coefficients.
I'm still wondering about the overall_best_*.* outputs - are these the really final output, or do we go for cycle_best_3.* series? The overall_best_xxx files are copied from the cycle_best_xxx files which are copied from the original files, all of which are in the TEMP0/ subdirectory.
Thanks for pointing out that the difference coefficients are not present in the autobuild map file. I will fix the output to have the original refinement map file available. All the best, Tom T