With XPAND: One of the problems when you are using strict NCS in your refinement and rebuilding is that it becomes very complicated to get an overview of all bad contacts, salt links, hydrogen and hydrophobic interactions generated by the combination of non-crystallographic and spacegroup symmetry.
The program XPAND (pub/gerard/xutil) now contains an option to explicitly generate a list of all these contacts and interactions.
It also attempts to classify interactions between C, N, O and S atoms, and it prints a flag for ("self") interactions between different copies of a residue. The classification involves disulfides, bad contacts, salt links, hydrogen bonds, hydrophobic interactions, close positive charges, close negative charges, and (too) close other interactions.
The option can also be used if your structure doesn't have any NCS, by supplying the identity operator as the only "NCS operator".
See the on-line manual for details and an example.