Nat,
I have been using the auto.ncs function in phenix, but I haven't really looked to see if they are properly defined myself.
Pavel,
At this point I have not tried using the ordered_solvent command in phenix yet to find waters. I will try that real quick before I bother you to have a look at it. I'll let you know the updated R's afterwards.
Gino,
It is interesting that you say that, because I after I lowered the symmetry to P21, and re-ran xtriage, it mentioned that I had pseudo-merohedral symmetry, but I didn't pursue that further. My beta-angle was also ~90.2 in this case, and the twinning operator is the same (h, -k, -l).
I will detwin and re-refine and see what happens,
Thanks everyone and I'll let you know what works,
Bret