Where can I set B-factor for water in phenix.refine on the GUI version of phenix?
Do you mean resetting the B-factors for all waters, or the B-factor for new solvent molecules when the water picking option is selected? For the latter, it is here:
Settings menu->Ordered solvent...->Initial B-factor value
(You may need to change the "user level" menu to "intermediate" or "advanced" if you don't see that control at first.)
If you want to reset B-factors for existing waters, open Settings menu->Model modifications->Modify ADPs, enter the selection for waters in the first control ("resname HOH" is usually all you need), and enter a suitable value in "Set isotropic B to:".
Of course in either case, by default phenix.refine will re-refine those initial values.
-Nat