I can confirm the problem.
If I take a previous successful refmac refinement, remove the initial N atom
from
the first residue in the input PDB file, and re-run the refinement I get:
Problem with the ADP of the atom N A 33 ADP is non-positive
-94.380859
Problem with the ADP of the atom N A 33 ADP is non-positive
-94.382088
starting already in CGMAT cycle 1.
Deleting instead the C-terminal O atom[s] does not produce an equivalent error.
CCP4 6.3: Refmac_5.7.0029
Nevertheless, in my test case the refinement ran successfully despite the error
messages.
Ethan
On Tuesday, July 24, 2012 09:54:26 am wtempel wrote:
> There are atom records for C, O and CA (B-factors 42, 43, 40A**2,
> respectively), but not for N, as density tapers off going to the amino
> terminus (well, without the "amino" in this case). Residue 3 is the
> lowest-numbered residue in its chain. B-factors of N, CA of residue 4 are
> 38, 33A**2, respectively. Could refmac just be taking exception to the
> missing N atom?
>
> ---------- Forwarded message ----------
> From: Ethan Merritt <merr...@u.washington.edu>
> Date: Tue, Jul 24, 2012 at 11:27 AM
> Subject: Re: [ccp4bb] Refmac: ADP is non-positive
> To: wtempel <wtem...@gmail.com>
> Cc: CCP4BB@jiscmail.ac.uk
>
>
> On Tuesday, 24 July 2012, wtempel wrote:
> > CCP4ers,
> >
> > a log file from Refmac_5.7.0027 presents me with this line:
> >
> > <fromLog>
> > Problem with the ADP of the atom N A 3 ADP is non-positive
> > -1.7740907E+35
> > </fromLog>
> >
> > I did not explicitely refine ADPs or TLS.
> > Should I modify my model when I encounter such a message? If yes, does the
> > message refer to a specific atom, such as atom N of residue 3 in chain A?
> I
> > should note that that atom is omitted from my model due to lack of
> electron
> > density/disorder.
>
> What do you mean by "omitted from the model"?
> Are there no ATOM records for that residue in the PDB file?
> What are the B factors for the other atoms in that region?
>
> Ethan
>
> >
> > Many thanks in advance,
> > Wolfram Tempel
> >
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
