INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqa_0942/12_2021/6lqa_0942.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 6lqa_0942.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for QDN
  Running eLBOW on QDN.cif
	3 ring group 6 6 6
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/build/../modules/elbow/elbow/command_line/ready_set.py", line 1104, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/build/../modules/elbow/elbow/command_line/ready_set.py", line 878, in run
    random_seed=working_params.ready_set.run_options.random_seed,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/build/../modules/elbow/elbow/command_line/ready_set.py", line 263, in run_though_all_the_options
    None),
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2485, in run
    hydrogens=hydrogens,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 781, in elbow_on_pdb_file
    silent=True,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/command_line/builder.py", line 2368, in run
    molecule = builder(molecule, options)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/command_line/builder.py", line 962, in builder
    molecule.OptimiseProgression()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/utilities/OptimiseMixins.py", line 865, in OptimiseProgression
    additional_restraints=additional_restraints,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/utilities/OptimiseMixins.py", line 705, in OptimiseCCTBXProgression
    additional_restraints=additional_restraints,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/cctbx_api/CCTBXMixins.py", line 246, in GetNewManager
    self.GetRestrainedParameters(additional_restraints=additional_restraints)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/cctbx_api/CCTBXMixins.py", line 301, in GetRestrainedParameters
    self.GetCCTBXRestraints(additional_restraints=additional_restraints)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/cctbx_api/CCTBXMixins.py", line 451, in GetCCTBXRestraints
    self.restraint_class += self.chiral_restraint[key]
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/cctbx_api/RestraintClass.py", line 254, in __add__
    chirals += other.GetChirality()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/elbow/elbow/cctbx_api/RestraintClass.py", line 647, in GetChirality
    ids.append(self.link[atom.index])
KeyError: 49