[phenixbb] XYZ refinement vs individual sites refinement

I am new to phenix and I am trying to probe two residues that are putative H-bond partners, after refinement they seem to be put in orientations that would make it impossible for them to be interacting with a ligand. My SA composite omit map may suggest that one of the Asn could be in a different position. My question: If I manually change its conformation is it wise to keep its position fixed during refinement to see what the new maps would look like? If so where would I do that under the real space or individual sites tab on GUI phenix? I am not sure what these 2 tasks accomplish exactly. Any guidance would be appreciated. Thanks Yuri Pompeu