Why am I having difficulty specifying a QSite QM region using backbone cuts?

Placing multiple cuts in the same residue or a cut in each of two adjacent residues is not allowed. For example, with a sequence of residues numbered 1, 2, 3, a pair of cuts could only be placed in residues 1 and 3. Cuts could not be placed in adjacent residues 1 and 2, or 2 and 3.

Starting with QSite 4.0, backbone cuts can be made in any peptide residue, including glycine, proline, and their adjacent residues, with the exception that cuts on proline (PRO) residues cannot be made between the N atom and the alpha C atom. QSite 3.0 and earlier versions do not allow backbone cuts in glycine residues, in proline residues, or in residues adjacent to proline.

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