[phenixbb] Real space refine of long side chains

Gyles Cozier gc234 at bath.ac.uk
Wed Nov 27 02:31:53 PST 2019


This sounds similar to the issues I have been having (but with x-ray data) from version 1.14 onward (Pavel I have previously sent you files regarding this, but can send again if you need). It happens for me even with high resolution (better than 2A) structures, but mostly with flexible side chains that have poor density. The side chains even push other residues (often symmetry related residues) out of their density. To me it seemed it might be connected to over zealous rotamer correction that began for me from version 1.14. As noted in the recent post 'Differences in refinement statistics', version 1.17 no longer gives me over corrected 0% rotamer outliers (versions 1.14-1.16 moved residues out of density to 'correct' rotamer outliers), but still pulls some side chains into the wrong density (although not as bad as versions 1.14-1.16). So currently I still use version 1.13 as later versions give me problems with side chains (unless I turn off real space refinement).

Bye for now,


From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
Sent: 26 November 2019 19:02
To: Leonid Sazanov <sazanov at ist.ac.at>; lp212 at cam.ac.uk <lp212 at cam.ac.uk>; PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Real space refine of long side chains


does anyone has a clear example that demonstrates this issue and that
you can share with me? Having such an example would be most helpful as
it will allow me to investigate the problem and hopefully address it

I suspect this can potentially happen at low resolution (perhaps 4-4.5A
and lower) when main-chain density looks like tubes and there isn't much
density for side chains, so the main chain density attracts side chains.
However, with default setting this should not happen as there are
rotamer restraints. So I'm still not sure what's happening and this is
why I'm looking for an example.


On 11/26/19 03:55, Leonid Sazanov wrote:
> Hi,
> We have addressed exactly this problem by writing a script, in which
> B-factors are refined first and only then real-space refinement happens.
> This allows disordered side-chains to acquire high B-factors and so
> they are not pulled into backbone anymore.
> This cycle is repeated twice to achieve convergence.
> Parameters for B-factor refinement (ADP restrains) were optimized to
> account for consistent lack of density for acidic side chains in cryoEM.
> It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
> If needed, I can send a script.
> Best
> Leonid

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