RuntimeError: Unexpected end of output."refine_65-coot-2.metal.edits"Error interpreting command line argument as parameter definition:I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message
Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions.