Dear Joanna, There might be an unnecessary TER card in your PDB file between residues 430 and 431 of chain A. Could you check that? The log file suggests that residues after 430 are being recognised as a non-polymer part.
Best regards, Keitaro On Mon, 3 Feb 2025 at 20:12, Joanna Zukowska <[email protected]> wrote: > > Good morning Eleanor, > > Thank you for your response, I have attached the log file. As far as I am > aware we are not requesting unrestrained refinement. > > Best wishes, > Joanna > ________________________________ > From: Eleanor Dodson <[email protected]> > Sent: 03 February 2025 10:47 > To: Joanna Zukowska <[email protected]> > Cc: [email protected] <[email protected]> > Subject: Re: [ccp4bb] Bonds Breaking After Refinement > > You don't often get email from [email protected]. Learn why this is > important > > CAUTION: This email came from outside of the University. To keep your > account safe, only click on links and open attachments if you know the person > who sent the email, or you expected to receive this communication. > > > > 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 > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
