3) When I ran phenix.refine, I found the following message in the log.

Number of residues, atoms: 32, 418 Unusual residues: {'NAG': 22, 'MAN': 10} Classifications: {'undetermined': 32}

"Unusual" means "not peptide, rna/dna, or water". It is just for information. If phenix.refine cannot find matching CIF restraint definitions, it will report "Unknown residues". Ralf