To either constrain or restrain to noncrystallographic symmetry the portions of the molecules which correspond to one another must be defined. In TNT this information is defined on the CLUSTER statement.
A cluster is a collection of chains, some portion of which have identical conformations. A cluster may contain many chains. Parts of each chain may belong to different clusters but no single residue may belong to more than one cluster -- The clusters must not overlap.
As an example consider a case where a hemoglobin molecule has crystallized in a form with one tetramer ( ) in the asymmetric unit. The two chains have the same structure, as do the two chains. However, even though the and chains are similar there are significant differences. One would not want to restrain them to each other. We are left with two clusters, one for the chains and another for chains. The CLUSTER statements for this case would simply be
CLUSTER ALPHA CHAINS A1 A2 CLUSTER BETA CHAINS B1 B2