Hi James,

Number of atoms with unknown nonbonded energy type symbols: 14 "CD CD D 1 " "CD CD D 2 "

This problem should be fixed in the latest phenix development release (1.26 beta @ http://www.phenix-online.org/download/index.html) and the slightly more recent CCI Apps (link at same web page). Are you using phenix.refine from an older release? Could you please try the latest phenix or CCI Apps? Ralf