phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/05_2023/6n58_0349_trim_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/05_2023/6n58_0349.map refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False >& 6n58.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/05_2023/6n58_0349.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n58_0349/05_2023/6n58_0349.map 3.78
Refinement ran but no refined model file.