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