Hmm, I used to think I understood this, but I'm feeling a bit dim right
now.
On 25/08/2011 11:07, Ian Tickle wrote:
Since the target function in MX refinement is the total likelihood
(working set + restraints), there's no reason whatsoever why any
another function, such as Rfree & LLfree, should have an extremum at
the same point in parameter space as the target function.
This is self-evident; what is not obvious is why the target function
should be having the final word. Wasn't the word "over-refinement"
introduced to describe exactly this: that the target function was
wrong? Isn't this the purpose of cross-validation, to use an
independent measure to judge when the refinement is /not/ producing the
"best" model?
Rfree is particular is problematic because it is unweighted, so poorly
measured reflections in the test set are going to have a
disproportionate influence on the result (e.g. see /Acta Cryst./
(1970). A*26*, 162).
This may be true; but as it is independent of refinement, is it not
nevertheless the only measure I should trust?
Or maybe what you intended to say: only trust refinements for which
Rfree decreases monotonically, because only then do you have a valid
choice of parameters.
phx.
