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. Another remedy might be to manually place the metal ion in position followed by zero cycles of refinement to get the final R-values. There is some evidence that excluding isolated atoms from refinement may introduce some systematic error on the rest of the structure, but it is likely very small. Cheers, Ed. On Wed, 2011-12-28 at 13:29 -0600, Dima Klenchin wrote: > Hello, > > I have a metal ion sitting on a two-fold. I assigned it an occupancy of 0.5 > but Refmac keeps refining it away from that position so that in the end > there is a symmetry-related ion 1.6A away. I thought that this problem has > been rectified long ago? Certainly I had several occasions where Refmac > would automatically recognize special position and automatically assigned > proper occupancy (1/n). Not sure why this particular case is different... > > This behavior is the same in: > > Refmac 5.5.0088 (Windows) > Refmac 5.5.0102 (Windows) > Refmac 5.6.0117 (Windows) > Refmac 5.5.0109 (Linux) > > I also tried leaving it at occupancy 1.0 and also tried renaming MN2+ to > water at occupancies of 0.5 and 1.0. All to no avail - the atom is always > shifted away from the density. > > Anything I can do to force Refmac to keep it nice and tidy? > > Thanks and Happy New Year! > > - Dima
