This
happens on the standard release and development version 1422.
Is there some way to turn off hydrogens as a work around?  Test files
available on request. : )

Unfortunately the problem is that phenix.refine always (for the last
couple of years) calculates the clashscore as part of coordinate
refinement, instead of simply using the nonbonded restraints as a
target, and the clashscore by definition takes hydrogens into account.
 So there is no way to entirely avoid adding hydrogens if you are
using the individual_sites strategy.

I can add a flag to disable reporting Molprobity statistics within phenix.refine: it's a trivial change. Currently it is always calculated, and in case of weight optimization it is actually used to select optimal weights.
Proper fix though is to make Probe or Reduce faster.

Pavel

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