I am using emdensity to refine my model. My pdb file contains HEME atoms and I need them to be refined as well. I used relax protocol with -edensity options and adding extra tags -extra_res_fa and -extra_res_cen. When I looked at the output file, I saw warnings showing "missing heavy atoms" along with "can't find pose atoms". Also. the pdb file does not seem reasonable, since the HEMEs were not quite sitting in the density. (This is a test run, so I only generated one structure). In addition, there is some error message such as core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!. I am wondering how I could fix this? I attched my bash file here.