[phenixbb] pdb file error

Hi Everyone, I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part. Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located" Does anyone know how to fix this problem? I tried converting the file into mmcif and feeding it to phenix but the same error comes back again. Thank you very much, Maher