[phenixbb] target bond/angle RMS deviations from ideal

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Mon Dec 11 09:42:51 PST 2017

On 11/12/2017 15:44, wtempel wrote:
> Hello all,
> the documentation <https://www.phenix-online.org/documentation/faqs/refine.html> states that
>     This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high
>     resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly
>     lower.
> I understand that exceedingly high RMSDs from ideal could indicate overfitting.

Do you mean _low_ RMSDs from ideal?

> On the other hand, local deviations from ideal geometry may point to correctable modeling errors,


> and I am 
> concerned that overly tight restraints may cause that diagnostic tool to become less sensitive, or local 
> errors to be spread in to the model.

Refinement (with conventional-style restraints) will try to "spread the load" to other geometric parameters 
- not only tightly-restrained refinement. A tightly-restrained structure will have less geometric 
distortions than a less tightly restrained one (as measured by the geometry against which the model is 
refined), so yes, a diagnostic tool designed to look for issues in geometric restraints will be less 
sensitive in that case (at least on the absolute scale, it is quite likely that they will nevertheless be 
larger than "neighbouring" restraints). In my experience looking at high resolution structures, there is 
less "real" distortions of side-chain angles than for the main-chain angles (bonds are not so noticeably 

> For what bond and angle rms deviations from ideal do my colleagues on the BB aim and how have they arrived 
> at those targets? Did my web search miss a relevant paper?

I don't know about that, but I see nothing with which I would disagree in the phenix.refine documentation. I 
would add though that, as a rule of thumb, the lower the resolution of the structure, the more the model 
should comport with known geometry (again, as measured by the geometry against which the model has been 


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