Hi,
Use different altloc tags in the PDB (Column 18). For example:
HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O HETATM 2143 O BLIG 1010 7.403 -7.755 -0.773 1.00 29.28 O
Then it will know they don't occupy the same space at the same time. As a word of warning the occupancy refinement of two proximal atom that don't have the same residue number can sometimes add up to more than 1 so check to make sure the model makes physical sense.
if you assign them the same residue number, in the example above that would be HETATM 2142 O AHOH 1009 1.332 -11.668 14.957 0.50 6.57 O HETATM 2143 O BLIG 1009 7.403 -7.755 -0.773 1.00 29.28 O then the sum of occupancies occupancy(AHOH) + occupancy(BLIG) will be 1 exactly. Please let me know if it is not the case. An example of similar thing is: http://www.rcsb.org/pdb/files/1EJG.pdb see residue number 22 for example. Although that software didn't do it quite right (I mean occupancy grouping and constraining). Pavel.