[phenixbb] "ATP" monomer in phenix_refine

Hi, I had a trouble of refining "ATP" in Phenix. I appreciate any help. ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA chain in coot as a monomer "ATP", and it could be connected to the downstream base after I changed the "_chem_comp.group" option to "RNA" in the cif file. But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer and didn't connect it to the downstream base. I tried two ways to solve it 1. Add the the modified (chang the "_chem_comp.group" option to "RNA") cif file in phenix_refine, but Phenix doesn't recognize it. 2. In REEL, I found phenix has its own cif file for ATP, but the its header couldn't be edited. Any suggestions? Thanks. Yu