INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbs_31519/12_2021/7fbs_31519.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7fbs_31519.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for 4Y4
  Running eLBOW on 4Y4.cif

MoleculeClass :  C:21  N: 1  O: 3 (CHEMICAL COMPONENTS format)
	52 atoms
	53 bonds
	92 angles
	129 dihedrals
	2 rings (groups, rings, atoms) 2 12
	1 chirals : R 

  Build ligand and use user provided restraints : 4Y4

  More than 20 percent of the atoms are missing for 6OU
  as compared to the Monomer Library

  More than 20 percent of the atoms are missing for 6OU
  as compared to the Chemical Components

  Build ligand and use monomer library to name atoms : 9Z9
Sorry: 
    Atoms in the input are supposed to be bound
     
    C23(9Z9) - C22(9Z9) = 2.88

    Fix the input file and retry

    EXITING