Refinement with minimization (selected part of model):
% phenix.refine data.hkl model.pdb strategy=individual_sites sites.individual="chain A"

This will refine the coordinates of atoms in chain A while keeping fixed the atomic coordinates in chain B.

So I think you probably need to have a different chain ID for your ligand, and the above should do the trick. Note that here, Phenix is run in command line mode, not the GUI. I haven't checked if it's possible to do this with the GUI.

In general, anything possible on the command line should be possible in the GUI as well.

If you right-click on the check-box for "Individual sites" (or any other strategy) in the GUI, it should pop up a menu that will give you access to the relevant atom selection(s). Alternately, go to the Settings menu and open Atom selections->Individual sites. The first control isn't labeled very well (I think it just says "Atom selection"), but that's what you want to use - following the example above, just enter "chain A". If you click the "view/pick" button, it will let you verify that the atom selection does exactly what you want, or you can pick selections with the mouse.

-Nat