phenix.real_space_refine /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd3_13329/12_2021/7pd3_13329_updated.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd3_13329/12_2021/7pd3_13329.map refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd3_13329/12_2021/7pd3_13329_ligands.cif >& 7pd3.txt failed.

/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd3_13329/12_2021/7pd3_13329.pdb /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd3_13329/12_2021/7pd3_13329.map 3.4
Refinement ran but no refined model file.