phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gup_9539/12_2021/5gup_9539.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gup_9539/12_2021/5gup_9539.map refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False >& 5gup.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gup_9539/12_2021/5gup_9539.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gup_9539/12_2021/5gup_9539.map 4.0
Refinement ran but no refined model file.