phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5q_5776/05_2022/3j5q_5776_trim.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5q_5776/05_2022/3j5q_5776.map refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False >& 3j5q.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5q_5776/05_2022/3j5q_5776.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5q_5776/05_2022/3j5q_5776.map 3.8
Refinement ran but no refined model file.