[buster-discuss] Exploding R-factors / adjustment of X-ray weight ?

Clemens Vonrhein vonrhein at globalphasing.com
Mon Feb 13 19:56:27 CET 2017

Dear Thomas,

On Sat, Feb 11, 2017 at 09:29:34AM +0000, Krey.Thomas at mh-hannover.de wrote:
> I am refining a 2.6A structure with a relatively large hexagonal
> unit cell (~260x260x200). There is no indication for problems in
> indexing (e.g., twinning) nor for pseudotranslation and the MR
> solution with 5 molecules per AU looks relatively clear (TFZ of
> ~31).

Is this the number of mol/asu you expect? How homologous/identical and
complete is your search model (i.e. is it just main chain? or
poly-ALA? or poly-SER?).

> Nevertheless, the refinement explodes to R-values of about 0.85,

This sounds very much like an incomplete (or very poor) starting

> but surprisingly the corresponding maps look quite reasonable (so
> the molecules do not seem to be placed simply wrong!).

Do you see where you need to correct your current model or where you
need to build new model? This would be a very good indication of the
predictive power of your current phases.

Can you send us the reciprocal space CC plot of that refinement,
e.g. after

  graph_autobuster_recipCC -d your-output-dir

This might enable us to see what the reason for those high R-values

> My question is, whether these high R-factors can be temporary and
> related to the adjustment of the X-ray weight and should go down at
> some point or if there is something more basic that I am doing
> wrong?

They can be temporary, yes. However they are unlikely to be related to
anything to do with the X-ray weight.  We've had multiple cases with
poor R-values (and increasing with refinement) while the reciprocal-
space CC plots showed values that stayed below a ceiling that was very
much less than 1.0, e.g typically 0.5-0.6 instead of the 0.8+ values
normally seen with a good model. Their meaning was therefore that the
model was systematically incomplete - that is why we want to take a
look at your RecSCC plots, to check whether this is the case with your

Best wishes

Clemens & Gerard (for buster-develop)

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