[phenixbb] XYZ refinement vs individual sites refinement

[Yuri]

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