Re: [phenixbb] question on bad geometry

This is a good point and it is often useful to prune back to poly(ALA) in doubtful regions which can help centre the backbone in the strongest density and then re-build sidechains afresh. All the best Martyn Martyn Symmons Cambridge UK --- On Wed, 1/9/10, Robert Immormino wrote:

From: Robert Immormino Subject: Re: [phenixbb] question on bad geometry To: "PHENIX user mailing list" Date: Wednesday, 1 September, 2010, 12:27 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,  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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