I was using AutoSol GUI for MR-SAD of my data and trying to  turn off "place waters in refinement". However, the output pdb files still got waters in them. I did check the run log file and confirmed both the "place_waters" and the "flood_with_waters" flags were set to false. But in the later session, it still recorded "adding waters in refinement". 

Is there any parameters I should adjust to avoid adding waters during the Autosol run. Or is it just turned on in the end in order to calculate R_work/free, and doesn't affect your phasing solution?

Look forward to your responses. Thank you in advance!