[phenixbb] question on bad geometry

[Robert Immormino]

Hi Fengyun,

Statistics like these mean that the backbone of your model is not
quite right, so re-building is necessary.  And Pavel can correct me if
I'm wrong, but I think fix_rotamer becomes increasing less successful
the further you have backbone from the correct position.  So first the
mainchain and then the sidechains need to be fixed.

Do the Ramachandran outliers bunch together in loop regions, or are
they distributed across the structure?

Most of the Ramachandran outliers in secondary structure regions in my
experience are due to having the peptide bond flipped.  Check closely
to see if you can find density for carbonyl oxygens, and remember in
alpha structure they point toward the C-terminus, and in beta
structure they alternate.

Loops are more difficult.  The only general rule I know is that
consecutive carbonyls tend to not point in the same direction....with
the major exception being metal binding loops.

Also it may be worth double checking the sequence register, especially
near ends of secondary structure elements.

Autobuild likely will take care of most of your issues, but a careful
eye toward rebuilding can give you confidence that you've got the
model right.

Good Luck,
-bob


On Tue, Aug 31, 2010 at 9:37 PM,  <fn1 at rice.edu> wrote:
> Hi everyone,
>
> I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. However,
> the geometry is not that good, the followings are the output from
> phenix.model_vs_data,
>
>    Stereochemistry statistics (mean, max, count):
>      bonds            :   0.0080   0.0547 3244
>      angles           :   1.1669  12.1085 4374
>      dihedrals        :  15.7241  85.6280 1202
>      chirality        :   0.0706   0.2831 536
>      planarity        :   0.0036   0.0246 573
>      non-bonded (min) :   2.1217
>      Ramachandran plot, number of:
>        outliers : 17    (4.02  %)
>        allowed  : 37    (8.75  %)
>        favored  : 369   (87.23 %)
>      Rotamer outliers        : 30 (8.62 %) goal: < 1%
>      Cbeta deviations >0.25A : 0
>      All-atom clashscore     : 40.51 (steric overlaps >0.4A per 1000 atoms)
>
> I tried to use fix_rotamer=True, but it doesn't help at all. As to the
> rotamer outliers, the value is far higher than the ideal one. Does that mean
> I need to manually adjust the model? Or will autobuild help improve the
> geometry?
>
> Thanks!
> Fengyun
>
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