When GEO_REF is used, the reference geometry is rotated and translated to give the maximum overlap with the data-set geometry.  In some systems, a further increase in overlap can be obtained by swapping pairs of atoms in the reference data-set.  An example would be to swap around two hydrogen atoms attached to the same atom, e.g., in a methylene or amine group.  This operation is done automatically.  To prevent automatic swapping, add NOSWAP.