I have a protein cocrystallized with a metal chelator complex. The side chain of a Asp residue has density around one of the chelators(oxygen atom). The positive density for the rotamer of Asp is seen too close to chelator oxygen(~1.17 A) and therefore rotamer is moving into a negative density.

When I correct the rotamer and refine, it again come back to the same place, due to repulsive forces I guess. then I moved ligand away and refined with corrected rotamer, but after refinement ligand is again back at the same position, as well as the rotamer. How can I fix this? Does this indicate that the ligand may not be there although I see some density for it(full density is seen ~0.79 sigma and partial density ~1.00 sigma). Also is this happening due to the memory of ligand position in phenix.