Hello,
this may perhaps fall under "garbage in, garbage out".
The following reflection results in the appended stack trace.
Would it be reasonable to instead just treat such reflection as missing?
Best regards,
Wolfram Tempel

<mtz.dmp>
                      RFREE         F_r1lo1      SIGF_r1lo1      DANO_r1lo1
              SIGDANO_r1lo1      F_r1lo1(+)   SIGF_r1lo1(+)      F_r1lo1(-)
              SIGF_r1lo1(-)      ISYM_r1lo1     IMEAN_r1lo1  SIGIMEAN_r1lo1
                 I_r1lo1(+)   SIGI_r1lo1(+)      I_r1lo1(-)   SIGI_r1lo1(-)
 20   4  54              11            None            None        -3.61389
                     15.223          19.349         9.78972         22.9629
                    11.6577               0        -227.641         69.6184
                   -205.607          83.633        -277.365         125.635

</mtz.dmp>

<trace>
Traceback (most recent call last):
  File "Blah/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 74, in run
    master_params=customized_master_params)
  File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 274, in __init__
    reflection_file_server = self.reflection_file_server()
  File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 793, in reflection_file_server
    err=self.log)
  File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_utils.py", line 448, in __init__
    force_symmetry=self.force_symmetry))
  File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_reader.py", line 209, in as_miller_arrays
    base_array_info=base_array_info)
  File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 502, in as_miller_arrays
    dataset=dataset)
  File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 610, in group_columns
    group = self.extract_delta_anomalous(*labels)
RuntimeError: cctbx Error: Invalid combination of values while extracting anomalous array from columns: F_r1lo1, SIGF_r1lo1, DANO_r1lo1, SIGDANO_r1lo1, hkl=(20,4,54) [tip: "phenix.mtz.dump --show_column_data file_name" is available for inspecting the MTZ file]
</trace>