Thanks for telling me that.. E On Mon, 3 Feb 2025 at 12:55, Keitaro Yamashita < [email protected]> wrote:
> 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/
