For standard omit map, do you mean using Phenix-> Maps -> Composite omit map. And omit map method: Anneal and map types: 2mFo-DFc. Thank you so much!
All I meant by "standard" was "omit ligand, leave bulk solvent calculation alone". It doesn't need to be a composite omit map - what you were doing originally using phenix.refine was sufficient (if unnecessarily slow), and this is exactly what reviewers (or P.I.s) tend to ask for.