phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/08_2023/3jcj_6559_neut_trim_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/08_2023/3jcj_6559.map refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/08_2023/3jcj_6559_neut_trim_ligands.cif >& 3jcj.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/08_2023/3jcj_6559.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcj_6559/08_2023/3jcj_6559.map 3.7
Refinement ran but no refined model file.