Dear Phenix community,

I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this?
 
This is a 1.6Å structure using Phenix version 1.6.1-353.

Many thanks for all your help in advance,

Joe.

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