That is VERY odd - can you send a log file?
And are you sure you arent accidentally requesting "unrestrained
refinement"?
In REFMAC that would be triggered by a keyword
REFI UNRE

Eleanor


On Mon, 3 Feb 2025 at 09:37, Joanna Zukowska <
[email protected]> wrote:

> Hi all,
>
> Currently my colleague and I are experiencing a problem with peptide bonds
> breaking after refinement. Has anyone else experienced this or knows how to
> fix this problem? Selecting detect and apply covalent linkages in the
> restraints does not help.
>
> Best wishes,
> Joanna
>
>
>
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