INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz3_15033/03_2024/7zz3_15033.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7zz3_15033.eff

    Ligand restraint generation using eLBOW, phenix.elbow
    

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

  Build ligand and use monomer library to name atoms : PYR
  Using monomer library entry PYR as template
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/elbow/elbow/command_line/ready_set.py", line 1117, in <module>
    run(args)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/elbow/elbow/command_line/ready_set.py", line 883, in run
    random_seed=working_params.ready_set.run_options.random_seed,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2486, in run
    hydrogens=hydrogens,
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 1916, in elbow_on_pdb_file
    residue_group_lookup[lookup] = False #atom_selection[lookup]=False
IndexError: list assignment index out of range