CNS defaults to excluding them. As for phenix, I am not entirely sure -
it seems that phenix.refine does too (fill_missing_f_obs= False), but if
you use the GUI then the fill in option is turned on.
In practice, it will be turned on for command-line phenix.refine too if you don't supply your own custom map definitions - actually it produces both "filled" and "unfilled" maps, but the former is what most users will see in Coot.
-Nat
