I would like to restrain the positions of ribose/phosphate atoms of
altloc 'A' to the positions of those in altloc 'B'. Problem is,
altloc A and altloc B are different residue types, so phenix.refine
exits stating that there are no common atoms when I enter the
following NCS-type restraint:

Wild guess - do you have a non-palindromic DNA helix bound in two different directions?

You can use the custom bond definitions to do this, but it's going to be messy. The documentation is here:

http://www.phenix-online.org/documentation/refinement.htm#anch80

You would need separate entries for each pair of atoms. I guess you'll want a distance_ideal of zero, and a small sigma (and perhaps slack). In the GUI, open Settings->Geometry restraints->Edit geometry restraints to add bonds. Might be easier to just write them out in a file and add that to the inputs list, however.

-Nat