No no no no no.  This would be true in the general case, but it is absolutely *not* a good CC for comparing local density, especially when judging LigandFit results.  A LigandFit CC > 0.8 is almost certainly correct, > 0.7 is probably correct but may have some misfit atoms or poor density, > 0.6 is maybe correct but frequently wrong, and < 0.6 is almost certainly wrong.  For comparing the refined model with 2mFo-DFc density, the thresholds are higher - a ligand with refined CC < 0.8 should be treated with extreme suspicion.

Obviously we need a better measure than CC!

LigandFit isn't really the appropriate tool for this - but I don't think there's actually an easy, automatic way to do what you want in Phenix right now.  You can run AutoBuild with the existing model defined as "ligands", but that's going to be very slow.

Although I'm a little surprised that AutoBuild didn't build any peptide - are you sure it isn't already in your model somewhere?  Or did it build something and you removed it?  If you didn't include it in the sequence file, it may be a random set of residues (AutoBuild's guess for the actual sequence).

-Nat