I've seen this happening to water molecules as well (in a somewhat
unpredictable fashion). In the latest refmac versions, you can try
harmonic restraints, although these will only slow down the atom drift,
as the target position is updated every cycle.
Perhaps you can use distance restraints against a dummy atom to fix the
metal ion in place.
Thanks, Ed!
Just in case anyone else has the same issue:
With Garib's help, I have forced the atom into its position by using
external distance restrains of zero length against the same
symmetry-related atom. The cause is unclear because the same program
handles special positions in another structure just fine. Here is the exact
command I used:
EXTERNAL DISTANCE first chain M residue 3 atom MN -
second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y
Occupancy set manually to 0.5.
- Dima
