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 monitoredA 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 = 1A 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 = 1A 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 = 1A
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 = 1A 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 = 1A 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 = 1A 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 = 1A 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 = 1B 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 = 1B 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 = 1B 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
> >
> >
> >
> > ________________________________
> >
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