Weakly delocalized systems are well described by a single dominant "reference structure" with weak contributions from "secondary" structures. The latter are built from the NBOs of the parent reference structure, so that only occupancy shifts (diagonal density matrix elements) are considered in the NRT variational optimization.
More strongly delocalized structures require two or more reference structures. In this case, the NBOs (and manifold of secondary corrections) must be determined independently for each reference structure, and the multi-reference NRT variational optimization involves the entire valence density matrix (rather than diagonal elements only). The present tutorial describes how to bypass the default NRTWGT threshold for reference selection (see Manual, Sec. B.8.2).