INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt4_0501/12_2022/6nt4_0501.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6nt4_0501.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : AJP
  Using monomer library entry AJP as template
	Difficulties in the ring structures may lead to problems later

  group index 8
change? False

ChiralClass
	Atom  C81(81) xyz:(-7.078, -3.649, -4.429)     
	Atom  C12(12) xyz:(-6.765, -2.692, -5.502)    S ring index: 7
	Atom  C11(11) xyz:(-7.201, -1.595, -5.028)    S ring index: 7
	Atom  C07( 7) xyz:(-7.788, -3.155, -6.543)    R ring index: 7
	Atom  C13(13) xyz:(-4.778, -2.799, -5.537)      ring index: 7

	not correct chiralisation
	Difficulties in the ring structures may lead to problems later

  Build ligand and use monomer library to name atoms : LHG
  Using monomer library entry LHG as template

  Build ligand and use monomer library to name atoms : Y01
  Using monomer library entry Y01 as template

  group index 6
change? False

ChiralClass
	Atom  HBD(59) xyz:( 0.394, -0.838, -1.088)     
	Atom  CBD(18) xyz:(-0.672, -0.274, -1.633)    S ring index: 1
	Atom  CAK(19) xyz:(-0.174, -0.043, -3.246)      ring index: 1
	Atom  CBF(17) xyz:(-0.640,  1.411, -0.772)    S ring index: 1
	Atom  CBG(12) xyz:(-1.587, -0.799, -1.485)    S ring index: 1

	not correct chiralisation
	Difficulties in the ring structures may lead to problems later

  Attempting to download Chemical Components file for 76F
  Running eLBOW on 76F.cif

MoleculeClass :  C:41  N: 1  O: 8  P: 1 (CHEMICAL COMPONENTS format)
	126 atoms
	125 bonds
	235 angles
	322 dihedrals
	0 rings (groups, rings, atoms) 0 0
	1 chirals : R 

  Build ligand and use user provided restraints : 76F
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 1108, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 882, in run
    random_seed=working_params.ready_set.run_options.random_seed,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 266, in run_though_all_the_options
    None),
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2487, in run
    hydrogens=hydrogens,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2027, in elbow_on_pdb_file
    line.name = atom.atom_name_in_input
AttributeError: AtomClass instance has no attribute 'atom_name_in_input'