Hi Michael,

I did notice that CCP4 6.2.0 outputs the mtz file with this column order:

H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2
F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2
IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-)
SIGI_S13E_X2(-)

This new F,SIGF,DANO,SIGDANO order explains why the four MTZ columns are combined into an anomalous array. (The phenix tools have been doing this for many years.)

Is this an actual problem for you?

You could use phenix.reflection_file_convert --non-anomalous to obtain a non-anomalous array.

In phenix.refine you can say force_anomalous_flag_to_be_equal_to=False.

Ralf