I think we need more info here, i.e. what are refinement strategies A and B.
If A is “weight 1.0” and B is “weight 0.1”, then perhaps weight 0.2, 0.3, 0.5 or 0.7 will give you most of the benefits of both.
If A is “with NCS” and B is “without NCS” or vice-versa, then changing the NCS restraints or removing some regions that do not follow it from the NCS definition might be in order. Or rebuilding regions in not-so-great density that are now different to be the same before refinement (if the NCS restraints are messing up the geometry of those).
Etc.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
> On 25 Jan 2016, at 21:52, Keller, Jacob <[log in to unmask]> wrote:
>
> Dear Crystallographers,
>
> I seem to have an artistic situation on my hands: the decision between R and geometry.
>
> Refinement strategy A:
>
> R/Rfree: 0.084/0.156
> RMSbonds: 0.025
> RMSlengths: 2.1995
>
> Refinement strategy B:
>
> R/Rfree: 0.136/0.177
> RMSbonds: 0.003
> RMSlengths: 0.338
>
> RSRZ scores or similar are not available in B, but there are 0 outliers in A.
>
> Do I just flip a coin? I am inclined to go for B, since the data are twinned and are therefore somewhat less information-rich than normal, so should perhaps be guided by the geometrical book values more than normal, but the Rfree is fully 2% lower in A. Also, the R/Rfree gap is probably too big in A. Any advice/input on how to decide? Having been chastened by the recent "questionable structure" thread and the vitriol against PDB pollution, I am trying to be especially vigilant.
>
> Jacob Keller
>
>
> *******************************************
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: [log in to unmask]
> *******************************************
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