[phenixbb] statistics output by phenix.refine

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu May 17 11:16:39 PDT 2007

> Are these maximum likelihood targets the normal maximum likelihood  
> function or the minus one?

We are using the maximum likelihood targets described here:

Lunin, V.Y., Afonine, P.V. & Urzhumtsev, A. (2002). Acta Cryst. A58, 270-282.
Lunin, V.Y. & Skovoroda, T.P. (1995). Acta Cryst. A51, 880-887.

> Should I expect an increase or decrease of the target?

Decrease. But see below...

> If the part of the restraints is not combined with  
> the x-ray part, the target is showing is not the actual target the  
> program is trying to maximize or minimize.

Yes, that's right.

> The values don't have a trend, at least I can't see a trend in my
> log file.

The x-ray target may go up since we refine x-ray target + geometry
target. The total will always go down (that's how the minimizer
works), but an individual contribution may go up a bit.


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