I have 4 Mn (2 Mn in each chain) in my protein structure. One Mn has 1 cordination with water, 1 cordination with His and 4 cordination with Asp. I model build the His in coot. Even this His is in bond range with Mn. But, when i refine this model in phenix. This His again flip other side (N terminal which has to cordinate with Mn goes to other direction). I am facing this problem only with His of A chain only while N of His of B chain are towards Mn only.
Is there any option in pehnix refinment where we can exclude a specific residue or atom in refinment??