There is a ligand residue in the structure that have its occupancy set
to 0.75. refine with default parameters apparently refines every atom
individually, so in the end I have a strange situation where ligand
atoms have different occupancies.
Of course, regular alternate conformers in the protein part of the
structure have single occupancy refined per residue.
Interestingly, when I place altLoc identifier "A" in front of the
residue name of the ligand, single occupancy value is refined (although
there is no second conformation). It settles down near 0.7 (close to
what I selected previously based on a traditional approach of
eliminating difference density and roughly matching B-factors of
hydrogen-bonded protein atoms with ligand), so apparently constraints
(e.g. total occupancy for all the conformers) are not applied.
Is this intentional behavior (I understand that groups can be defined in
the input file but adding altLoc letter seems like a simple trick)? I
think most people would initially expect that occupancy will not vary
within a residue, so the default behavior may seem like a bug to some
(the only situation I can think of where such variation is justified is
to model radiation damage).
--
Ed Pozharski