[phenixbb] target bond/angle RMS deviations from ideal

Dale Tronrud detBB at daletronrud.com
Mon Dec 11 09:16:20 PST 2017

   The documentation you quote is specifically referring to a
"well-refined protein structure".  When you deposit your model it will,
one hopes, not contain "correctable modeling errors".  What you do
during refinement is a separate matter.

   For the very reason you describe, it is often useful to allow poor
geometry at times during refinement.  Simulated Annealing is the
ultimate as the model can look pretty ugly at high temps.  It may not be
common practice, but I consider an unusual amount of movement of a
residue while the geometry is relaxed and tightened again to be a flag
suggesting additional scrutiny during model building.

   When there is a significant conformational error in the model the
geometry of the atoms is often distorted, as you note.  I've found that
the same groups of atoms tend to stand out regardless of the tightness
of the restraint.  With a stronger weight the deviations are smaller on
an absolute level, but they are deviations non-the-less.

   This brings us to Z scores.  Judging a model based on rmsd Angstrom
or rmsd degree is quite problematic.  The method has a long history but
we are well past the time when it is the best.  Particularly for angles,
there are some restraints which are tighter than others.  In the E&H
library the NCaC angle has a SD of 2.8 deg while the internal angles in
the Phe ring are able 1.7 deg.  A one deg deviation in one is quite
different than one deg in the other.  The deviations need to be normalized.

   Note that a 2.0 deg SD is too tight for NCaC while too loose for the
Phe ring.  At high resolution, where you don't need geometry restraints
on the well ordered parts of your model, you will be penalized for your
perfectly okay main chain bond angles.

   If you have an angle with a 3 SD deviation from expectation you
should have a look and it doesn't matter if the standard deviation is 1
or 2 degrees.  That standard deviation is from the library and not the
rmsd of your model.

   In the end your model should be around 1 rms delta/sigma if your
resolution is so high that restraints don't matter and lower if you have
more typical resolutions.  How low depends on the "quality" of your data
and I'm not sure anyone has a measure of that that I find useful.
Empirically one minimizes the free R to set the strength of the restraints.

Dale Tronrud

P.S. For angles particularly, it is usually observed that very high
resolution models have bond angles deviations of greater than one.  The
Andy Karplus lab has published the view that the E&H library
underestimates the quantity of angle variability.  His new Conformation
Dependent Library for protein main chain is normalized better and very
high resolution models are scored more reasonably.  (Disclaimer: I've
been involved in this project.)

On 12/11/2017 7:44 AM, 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.
> 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.
> 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?
> Thank you in advance.
> Wolfram Tempel
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list