Dear Eleanor, > From log: refmac thinks there are 433 (A) or 426 (B) residues > but the VDW restraints seem to involve higher number residues . (of course > you may not have numbered things from 1...) > But why does it think the ligands include peptides??
This is because gemmi (which generates restraints within the refmacat scheme) interpreted everything after residue 430 of chain A as ligand, presumably due to an incorrect TER card. H2/H3 atoms (attached to N atoms in the main chain) were also generated incorrectly because these residues were treated as "ligand" (outside the polymer; otherwise, only "H" atom should be generated). Best regards, Keitaro On Mon, 3 Feb 2025 at 21:39, Eleanor Dodson <[email protected]> wrote: > > Hmmm = Keitaro is right - there is something odd for the last few residues.. > I would look carefully at the input coordinates about 430 > > From log: refmac thinks there are 433 (A) or 426 (B) residues > but the VDW restraints seem to involve higher number residues . (of course > you may not have numbered things from 1...) > But why does it think the ligands include peptides?? > > And why does REFMAC think this?? 25 chains?? Each of the last few residues > must be seen as a separate chain.. > Noted: A + B + C +14+8 = 25 > > ------------------------------------------ > Number of chains : 25 > > Thinking this is a bad VDW contact - A 430 CYS C . - A 431 GLN H3 - > will mean REFMAC wants to blow those residues apart.. > > Check the coordinates input to COOT and those output.. > You havent inserted an EDO or PEG with inappropriate numbering? > > > Creating restraints.. > > Chain info: > chain A > PeptideL: -2..430 (433 residues) > ligands: GLN HIS GLU ASN GLY PRO ARG EDO (14 residues) > chain B > PeptideL: -1..430 (426 residues) > gap between 306(THR) and 309(SER) > gap between 325(GLU) and 330(LYS) > ligands: PEG HIS GLN EDO (8 residues) > chain C > ligands: HOH (215 residues) > > > > **** VDW outliers > **** > > VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored > > A 430 CYS C . - A 431 GLN H3 . mod.= 0.582 id.= 2.950 dev= -2.37 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 431 GLN C . - A 432 ARG H3 . mod.= 0.569 id.= 2.950 dev= -2.38 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 433 PRO C . - A 434 GLY H3 . mod.= 0.547 id.= 2.950 dev= -2.40 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 434 GLY C . - A 435 GLU H3 . mod.= 0.528 id.= 2.950 dev= -2.42 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 435 GLU C . - A 436 ASN H2 . mod.= 0.673 id.= 2.950 dev= -2.28 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 447 HIS C . - A 448 HIS H3 . mod.= 0.829 id.= 2.950 dev= -2.12 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 448 HIS C . - A 449 HIS H3 . mod.= 0.489 id.= 2.950 dev= -2.46 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > A 449 HIS C . - A 450 HIS H3 . mod.= 0.849 id.= 2.950 dev= -2.10 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > .... > B 318 LYS HD3 . - B 331 PHE HE1 . mod.= 0.971 id.= 2.400 dev= -1.43 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > (This one is probably correct..) > > B 448 HIS C . - B 449 HIS H3 . mod.= 0.529 id.= 2.950 dev= -2.42 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > B 449 HIS C . - B 450 HIS H3 . mod.= 0.835 id.= 2.950 dev= -2.11 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > B 450 HIS C . - B 451 HIS H3 . mod.= 0.932 id.= 2.950 dev= -2.02 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > B 451 HIS C . - B 452 HIS H . mod.= 0.542 id.= 2.950 dev= -2.41 > sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 > > > > > > On Mon, 3 Feb 2025 at 11:21, Keitaro Yamashita > <[email protected]> wrote: >> >> 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/ ######################################################################## 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/
