Hi Yuri,

If tell phenix.refine to do occupancy refinement on resname HOH, will it still perform the default refinement for residues with alternate conformers?

Yes. It will add whatever selection you specified to the default selections. Note, that would apply to only existing waters with HOH resname. Occupancies of newly added waters (with ordered_solvent=true) will not be refined. To refine their occupancies as well you need to set True the corresponding parameter under ordered_solvent {...} scope of parameters. Pavel.