Re: [phenixbb] RMS angles and comprehensive validation in phenix

If the RMS of angles are so deviant and the structure is high resolution then wouldn't it show up in COOT density fitting? On Fri, Sep 19, 2014 at 12:50 PM, Katherine Sippel < [email protected]> wrote:

This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

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. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine wrote:

...

Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

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