I am just wondering whether there is a tool/feature in Phenix that (i) prints out all bonds/angles deviating by some specified number of standard deviations, and (ii) reads a user-defined .cif file for ligands as well so that this ligand appears in (i) as well. Phenix.pdbtools prints a bond histogram and I did not manage to include an external .cif file.

Most likely this is easy to do and I haven't found it in the manual yet.