“Rigid Body Fit Zone” from the “Model/Fit/Refine” dialog provides rigid body refinement. The selection is zone-based 1. So to refine just one residue, click on one atom twice.
Sometimes no results are displayed after Rigid Body Fit Zone. This is because the final model positions had too many final atom positions in negative density. If you want to over-rule the default fraction of atoms in the zone that have an acceptable fit (0.75), to be (say) 0.25:
(set-rigid-body-fit-acceptable-fit-fraction 0.25)