Hi Jan,
An Arg side chain is located very close to a crystallographic 2-fold. There is good evidence that the side chain has two conformations. However, because of the 2-fold, conformer A overlaps with its symmetry mate A*, as does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out of the density, same for B and B*.
Is there a way to avoid this without reducing the symmetry? In the real crystal, of course the two side chains are agnostic as to if they are called A or B and will avoid one another ...
you can exclude involved residue from repulsion by using this parameter: custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and (altloc A or altloc B)" You can do this in the GUI too by using search parameters option. Let me know if it doesn't do it and I will think of an alternative solution. Pavel