phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/06_2022/7xji_33228_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/06_2022/7xji_33228.map refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/06_2022/7xji_33228_ligands.cif >& 7xji.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/06_2022/7xji_33228.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xji_33228/06_2022/7xji_33228.map 3.9
Refinement ran but no refined model file.