[phenixbb] phenix.refine special positions

[Ralf W. Grosse-Kunstleve]

Hi Simon,

To add to the previous answers, note that phenix.refine currently
doesn't work well if you want to allow symmetry copies of your ligands
to overlap. If you move to individual coordinate refinement you have
to fix such ligands; i.e. it won't automatically repair bonds distorted
by rigid-body refinement. Removing this limitation is on my to-do list.

Ralf