INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz2_15032/06_2024/7zz2_15032.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 7zz2_15032.eff Ligand restraint generation using eLBOW, phenix.elbow 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-5370/build/../modules/elbow/elbow/command_line/ready_set.py", line 1117, in run(args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2486, in run hydrogens=hydrogens, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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