> and R-factor/R-free have a value of 0.328/0.326.
Notice that Rfree<R. This may be caused by twinning and/or NCS, as the
test set is not truly independent of the working set.
> The question is, as I only have ~3000 reflections, and the atoms in
> the sequence is around 1000, and each atom there are 4 parameters to
> be refined(X,Y,Z,B-factor, assuming occupancy is 1), so how to refine
> my model to avoid over-refinement?
Normally, at 3.2A you would have strong geometry restraints, thus
reducing the effective number of degrees of freedom to perhaps as few as
two per residue.
> Should I trust the electron-density map of the refined mtz data, or
> should I adjust the local geometries using Coot rotamers tools?
Not sure what you mean by this. Given the resolution and overall B
values, it is likely that you won't have strong enough electron density
to place many side chains. In which case you should omit the atoms
unsupported by electron density from your model. As a general rule, at
3.2A you should be able to trace the backbone and place some sidechains.
> How to set a reasonable B-factor values in the refinement?
The B-factor values are what they are, you cannot "set" them to a
reasonable value of your choice. It is not entirely unusual to see
B~100 at 3.2A, so don't worry too much about that.
Cheers,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
