phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/03_2023/6xit_22200_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/03_2023/6xit_22200.map refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/03_2023/6xit_22200_ligands.cif >& 6xit.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/03_2023/6xit_22200.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xit_22200/03_2023/6xit_22200.map 3.3
Refinement ran but no refined model file.