Re: [phenixbb] phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?

What is the refinement target ml_sad?

This instructs phenix.refine to use a target function from phaser. This option is still under development. You're better served with the ml target. (I hope Tom will help with the other questions.) Ralf