Hi,

thanks for your questions!

1) What's the reason for refining bss, xyz and adp in separate cycles?  CNS
does that too while refmac (I believe) refines them simultaneously.  I
suspect I missed something, but I thought the power of ML refinement is that
no refinable parameters are held constant if they're not supposed to be.
(At least, wasn't that the big deal in Sharp when it came out?)

It is common practice to refine bulk solvent and scale, coordinates, ADPs, an other parameters separately. There are numerical issues behind this (see for example: Acta Cryst. (1978). A34, 791-809; Acta Cryst. (2005). D61, 850-855; ...). CNS does exactly the same: it refines this parameters separately. To my knowledge, same for REFMAC. This is not target specific. The power of ML refinement is that ML target statistically models missing scatterers in a model and and errors (Acta Cryst. (2002). A58, 270-282).

2) How does one figure the right restraint weights?  (wxc and wxc).  In
refmac, I've always calibrated the weight with rmsd(bonds), tightening it
until rmsd(bonds) is ~0.018 (or below for lower reso);  invariably this is
where Rfree will decrease furthest and smoothly as well (i.e. without that
silly rise at the end.)

With phenix.refine I'm finding that I only get Rfree to drop monotonously
when I tighten the weights (both wxc and wxu) so much that rmsd(bonds) goes
down to ~0.002.  Would there be a different way to do this?

The weights wxc for coordinates (refinement target E = wxc*Exray + Echem) and wxu for ADP (refinement target E = wxu*Exray + Eadp) refinement are determined automatically based on the gradients ratio (Proc. Nat. Acad. Sci. USA. 1997, 94:5018-5023.). Again, this is very close to what CNS does and is demonstrated to be relatively reliable. Since it is automatic, it may give different weights from macro-cycle to macro-cycle making it possible some slight oscillation in R/Rfree. You can also scale the weights manually by using wxc_scale and wxu_scale to achieve desired gap between R and Rfree and deviations from ideal values of bonds, angles (see phenix.refine Documentation).

3) There isn't currently torsional refinement, is there?

It is under active development.

4) Is there good documentation for all the loads and loads of keywords?  The
names themselves are just descriptive enough to be interesting, but
obviously not enough to be informative if I don't just want the black box.

Many of the important and popular scenarios and keywords are in phenix.refine Documentation. I plan to expand it before the next release.

Please let me know if you have any questions.

Pavel.