Is the format from phenix.refine ready for deposit?



I believe so, but Pavel may be able to clarify this.

Yes, phenix.refine always outputs a PDB file with formatted REMARK 3 records containing data, model and model-to-data fit statistics that should be deposited to PDB. All you need to do is to remove plain REMARK records, from the very first line down to where the REMARK 3 ones starts.

Pavel.