I want to use phenix.ligand_identification to identify a ligand. I used chimera's volume eraser to erase everything except for the ligand density. I then converted it to mtz. in the phenix.ligand_identification gui, I set reflection data type to difference map. When I ran the job, I got a lot of "Sorry, resolve was not able to finish on the first cycle".

Regarding the mtz, I have to contour the map to 170rmsd to visualize it in coot, so something have to be wrong. I appreciate any input. 

Best regards.