I don't think so.  You'll probably find it easier to refine the atoms separately, i.e. one run with reference model and the individual sites selection set to "not resname HOH", followed by a run with harmonic restraints on waters and selection "resname HOH".  Alternately, you could try applying harmonic restraints to the entire model, although I suspect that the waters and protein require different weights (or sigmas).

-Nat