[phenixbb] fixing geometry for deposition

Kendall Nettles knettles at scripps.edu
Tue Nov 17 14:04:46 PST 2009

Hi Raja,
I would like to add to Pavel's excellent advice and ask if you have tried TLS refinement? It always improves the model in our hands, and in most structures ( http://journals.iucr.org/j/issues/2009/03/00/he5437/index.html ). You might also consider excluding the regions with poor geometry from the NCS groups, to see if they are in fact different. You are also forcing NCS regardless of the RMS distance. I would refine a few rounds without NCS and with the default refinement parameters, and then then turn the NCS back on. Look in the .geo file for excessive distances, and examine these regions in Coot using the NCS ghosts and maps to decide if they should be excluded from the NCS groups.

Another suggestion would be to try the kicked maps, or generate  composite omit maps to look at the regions with poor geometry.

You might need to subtly change half a dozen residues surrounding the geometry outlier to fix the problem. This might be done with simulated annealing, or try  autobuild in place.

Lastly, if its only a few residues, you can't fix it, and the maps support your model, don't worry about it.

Best Regards,
Kendall Nettles

On 11/17/09 3:02 PM, "Raja Dey" <rdey at usc.edu> wrote:

Hi Pavel,
              I used the following commands at the last stage of refinement:

phenix.refine 1205A-p21212.mtz nov138_001.pdb simulated_annealing=false ncs_groups.params main.ncs=true ncs.find_automatically=false refinement.ncs.excessive_distance_limit=None main.bulk_solvent_and_scale=false strategy=rigid_body+individual_sites xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=1 output.write_maps=true output.prefix=nov139 --overwrite

Regarding amino acids phy, psy..... I tried real space refinement/regularization in coot, but getting the same list of amino acids again and again in the pdb validation summary letter. I also tried mutation on its own to get the ideal geometry, still got the same result.

Did I do anything wrong?


----- Original Message -----
From: Pavel Afonine <PAfonine at lbl.gov>
Date: Tuesday, November 17, 2009 11:50 am
Subject: Re: [phenixbb] fixing geometry for deposition
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> Hi Raja,
> >                      pdb validation summary letter gives a list
> of covalent bond angles greater than 6 times standard deviation for
> dna part of my molecule. I am wondering if someone can tell how to
> fix that. I used PHENIX to refine my molecule. I did not use any
> restraints for the dna part.
> >
> did you completely turn off all the geometry restraints for that
> selected part of your structure? If so, then it is not surprising
> that
> it got distorted during refinement at 2.9A resolution, and
> therefore I
> would suggest re-running phenix.refine using all the restraints
> that
> phenix.refine normally uses by default.
> >                      Also a few amino acids are listed for which
> phy and psy fall outside Ramachandran plot. I like to know what is
> the best way to fix these phy, psy angles.
> >
> 1) Can't you do it in Coot? (especially when there are only a few
> such
> outliers, as you say).
> 2) Try adding riding H atoms and re-run phenix.refine (with and w/o
> weights optimization to see which option gives better results).
> 3) Try a quick geometry regularization going into trying "2)".
> Repeat
> the same with and w/o H.
> This is a pretty frequent question, so I hope someone someone can
> tell a
> success story about it...
> > Final refined parameters are
> >
> > REMARK Start: r_work = 0.3576 r_free = 0.3345 bonds = 0.009
> angles = 1.344
> > REMARK Final: r_work = 0.2517 r_free = 0.2845 bonds = 0.008
> angles = 1.209
> >
> > at 2.9A resolution
> Looks reasonable given the resolution...
> Pavel.
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