It may happen that, due to crystal contacts, there is found to be a structural difference between the two chains in the region of residues 100 to 125. These residues should not be restricted by the noncrystallographic symmetry, because the symmetry does not apply. You can use the RESIDUE modifier on the CLUSTER statement to specify only those residues which should be restricted. In this new case the CLUSTER statement for the ALPHA cluster would have to be altered, resulting in the new statements:
CLUSTER ALPHA RESIDUE 1 - 99 RESIDUE 126 - COOH CHAINS A1 A2 CLUSTER BETA CHAINS B1 B2
If you have noncrystallographic symmetry of this type and you execute the gather command, only the residues covered by the noncrystallographic symmetry will be gathered. The new ALPHA chain will only contain residues 1 thru 99 and 126 to the end. Chains A1 and A2 will retain residues 100 thru 125.