[phenixbb] Very low rmsd bond length

Pavel Afonine pafonine at lbl.gov
Tue Jul 25 18:20:19 PDT 2017


weight optimization searches for refinement strategy that results in 
smallest Rfree, yet acceptable other metrics, such as Rfree-Rwork gap or 
geometry measures, etc. Bond length RMSD that you got are likely what 
data wanted. After all, can you really distinguish a difference of 1/10 
of an Angstrom or smaller in 2.8A resolution map? So the smaller RMSDs 
the less your model overfits the data. I'd say "very low" is probably 
not "vary bad" at this resolution.


On 7/25/17 15:52, Mark Saper wrote:
> Hi all,
> A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased.  The weights were calculated with “Optimize XYZ Weight” option turned ON.  This seems to be the case with all of the structures that I have refined during the past 5 years.  My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights.  Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful).
> How do I address the reviewer’s concerns?
> Thanks,
> Mark

More information about the phenixbb mailing list