Re: [phenixbb] Real space refine of long side chains

Hi, 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, Gyles. ________________________________ From: [email protected] on behalf of Pavel Afonine Sent: 26 November 2019 19:02 To: Leonid Sazanov ; [email protected] ; PHENIX user mailing list Subject: Re: [phenixbb] Real space refine of long side chains Hi, 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 centrally. 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. Thanks, Pavel 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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