INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxg_13702/01_2022/7pxg_13702.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7pxg_13702.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

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

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

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

  Attempting to download Chemical Components file for 8H5
  Running eLBOW on 8H5.cif
	Difficulties in the ring structures may lead to problems later
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/build/../modules/elbow/elbow/command_line/ready_set.py", line 1104, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/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-1.20-4459/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-1.20-4459/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2485, in run
    hydrogens=hydrogens,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/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-1.20-4459/modules/elbow/elbow/command_line/builder.py", line 2368, in run
    molecule = builder(molecule, options)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/command_line/builder.py", line 918, in builder
    molecule.Ringise()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/RingTopologyMixins.py", line 91, in Ringise
    self.Generic_Ringise(allow_boat_conformation=allow_boat_conformation)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/RingTopologyMixins.py", line 329, in Generic_Ringise
    self._add_dihedrals_to_aromatic_rings()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/RingTopologyMixins.py", line 311, in _add_dihedrals_to_aromatic_rings
    if abs(dihedral.value())<10.:
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/DihedralClass.py", line 77, in value
    return self[0].xyz.BondDihedral(self[1].xyz, self[2].xyz, self[3].xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/xyzClass.py", line 480, in BondDihedral
    return sign*crossABC.Angle(crossBCD)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.20-4459/modules/elbow/elbow/chemistry/xyzClass.py", line 383, in Angle
    raise RuntimeError("zero bond length")
RuntimeError: zero bond length