Hello,

How can I successfully execute the following command:

phenix.refine pdb_1jbe_res_ALA_resID_101_del.pdb 1jbe.mtz main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite

Currently, I am getting the following error:

Sorry: Fatal problems interpreting model file:
Number of atoms with unknown nonbonded energy type symbols: 8
Please edit the model file to resolve the problems and/or supply a
CIF file with matching restraint definitions, along with
apply_cif_modification and apply_cif_link parameter definitions
if necessary.

I'm not a crystallographer, so I don't fully understand the error.

I'm simply trying to automate this procedure for many PDBs, and this particular error has come up quite a few times.
Can I resolve this issue by providing additional files or command line flags?

Other files I have available are 1jbe.cif and 1jbe-sf.cif.

File 'pdb_1jbe_res_ALA_resID_101_del.pdb' is similar to 1jbe.pdb, except that the occupancies for ALA 101 are set to 0.

Thanks,
Alex