% phenix.refine data.hkl model.pdb strategy=occupancies occ.params

occ.params
refinement {
  refine {
    occupancies {
      individual = element BR or water
      individual = element Zn
      constrained_group {
        selection = chain A and resseq 1
      }
      constrained_group {
        selection = chain A and resseq 2
        selection = chain A and resseq 3
      }
      constrained_group {
        selection = chain X and resname MAN
        selection = chain X and resseq 42
        selection = chain X and resseq 121
      }
      remove_selection = chain B and resseq 1 and name O
      remove_selection = chain B and resseq 3 and name O
    }
  }
}