Then how you ended up having anomalous data set for your neutron observations: FO,SIGFO,DANO,SIGDANO,ISYM ?

As I mentioned in my original mail, I've discovered that SCALA always outputs I+ and I- no matter what you do. From the manual:

"Normally anomalous scattering is ignored during the scale determination (I+ & I- observations are treated together), but the merged file always contains I+ & I-, even if the ANOMALOUS OFF command is used."

Thus if you don't take special precautions, e.g. in TRUNCATE, these will be converted to F+ and F- and (I now know) phenix.refine will use them. However I've now discovered that the keyword ANOMALOUS NO in TRUNCATE will prevent output of the anomalous columns altogether.

All in all, if you don't have anomalous data make sure your inputs files do not have spurious (anomalous) arrays: phenix.refine can't read your mind to see what you have done in your diffraction experiment - it's beyond the scope of what it's supposed to do!

Fine, I've now learned an important lesson in input/output checking! But could I politely suggest that an improvement in phenix.refine's mind-reading capabilities: if the user mistakenly inputs a file as neutron data with anomalous columns in, then these should be ignored, as the concept is by default incompatible with neutron data?

Finally, it would also be nice if the neutron maps and not just the X-ray maps were displayed in Coot during refinement and if the summary panel at the end of refinement showed statistics for the neutron data as well as for the X-ray data.