[phenixbb] Finding correct Se sites with autosol

Dear all, I have a 3 angstrom structure which I am trying to solve with MAD or SAD. The structure was previously solved with molecular replacement but refinement could not continue due to poor phasing at the N-terminal domain of the protein. I have run solve and autosol which are able to find the Se sites. However, Se sites are not anywhere near the methionines when I superimpose the ha.pdb and the pdb file that I obtain from a new run of molecular replacement. The exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show any connected densities. I have also tried autobuild with the solutions from AutoSol, but the model that it builds in is incorrect. Any suggestions would be appreciated. Thank you, Yu Seon Chung