phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/05_2022/3jcn_3285_neut_trim_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/05_2022/3jcn_3285.map refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/05_2022/3jcn_3285_neut_trim_ligands.cif >& 3jcn.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/05_2022/3jcn_3285.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcn_3285/05_2022/3jcn_3285.map 4.6
Refinement ran but no refined model file.