I was refining a structure containing L-hydroproline (HYP) and it looks like that the dictionary for HYP in Phenix has the wrong stereochemical restraint. I modeled as L-hydroxylproline (trans) but the phenix.refine always flipped the hydroxyl group and ended up as L-allo-hydroxylproline (cis).

I created a .cif file and the issue is resolved, but it would be nice if the restraint can be fixed in the next version of Phenix. 

Thanks a lot 

Yang Hai

Department of Chemistry, 

University of Pennsylvnia