[phenixbb] Occupancy refinement troubles

[Kieft, Jeffrey]

Hello All,

Question about occupancy refinement. I'm refining an RNA structure at 2.0 Angstrom resolution with bound ligands iridium hexammine and spermine. The location of the former can be confirmed in an anomalous difference map, but they are likely not full occupancy...likewise the spermine is likely less than one. When I use occupancy refinement, it leaves the RNA at full occupancy as expected, but refines each atom of the irhex and spermine individually, in some cases driving the occupancy to 0 for some atoms. 

It seems like this was an issue in the past, but I'm still seeing it. Any ideas? Could if be that Phenix doesn't recognize those ligands? Parameter files wrong?

Thanks for help!

Jeff