phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/05_2023/6vgn_21198_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/05_2023/6vgn_21198.map refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False >& 6vgn.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/05_2023/6vgn_21198.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgn_21198/05_2023/6vgn_21198.map 3.1
Refinement ran but no refined model file.