Dear Sean,
What a negative LLG combined with a large Z-score usually means is
that the answer is correct, but that the model doesn't predict the
data as well as expected. One possible reason is that you told Phaser
that the model is better than it really is (e.g. provided identity
values
maybe my message was a bit abrupt, what I meant was:
- if it (auto)builds using the real sequence and refines, you are sure
to have found the right solution. At 2.0 Angstrom this should only
take a few hours.
- if it doesn't, you may still have the right solution, but perhaps
you made a mis
try building (an autobuilding program like Arp-Warp comes to mind) and
refining the structure, then you'll know that you've solved the
structure for sure (or not).
or, if you'll permit a tongue-in-cheek reply:
stop bragging now, build and refine the structure, write the paper,
publish it and
I have a 2.0A data set that I solved using an ensemble of 5 related
structures in Phaser. My Z-scores for the solution are fantastic (RFZ=
28.7, TFZ=24.6), but my LLG is very negative (-698.2). The LLG increases
by almost 800 (started at -1488.6) during the course of the run. The
density for th
