INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7she_25125/01_2022/7she_25125.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7she_25125.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for PII
  Running eLBOW on PII.cif

MoleculeClass :  C:42  O:13  P: 1 (CHEMICAL COMPONENTS format)
	136 atoms
	136 bonds
	261 angles
	382 dihedrals
	1 rings (groups, rings, atoms) 1 6
	7 chirals : R Auto R R Auto S R 

  Build ligand and use user provided restraints : PII

  Build ligand and use monomer library to name atoms : CLR
Sorry: 
    Atoms in the input are supposed to be bound
     
    C9(CLR) - C11(CLR) = 1.88

    Fix the input file and retry

    EXITING