phenix.refine does not use REMARKS.

Actually it uses some information from REMARK records (if it finds it and validates it is good, otherwise continues), such as TLS selections, twin operator, perhaps something else which I forgot.

Recently it started outputting LINK records for internally generated extra restraints, such as metal coordination or ligand linking. I can't remember if we read them back and if we do what happens if LINK defines nonexistent (obsolete) atoms.

Pavel