`extract_topology`: Specify nets that are Non-crystallgraphic

[KunhuanLiu]

Nets such as nts are non-crystallographic and will lead to an error message in the current version of Systre:

#!!! ERROR (STRUCTURE) - - Structure has collisions between next-nearest neighbors. Systre does not currently support such structures..

The message can be improved to suggest more details behind the error considering the MOF topology. NU-110: SingleNode gives nts topology (confirmed using Simplified Topology with Two Conn.cif)