Hi Jon & Robbie,
Yes, that did the trick. I must have missed the whole discussion on how treatment of carbohydrates has changed since I refined this glycosylated protein. Strangely, Refmac still complains that OXT is missing from every residue in the structure, but at least it doesn't bomb out now and the refinement runs to completion.
Thanks for your rapid answers!
Derek
On 28 Nov 2018, at 17:29, Jon Agirre <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Derek,
does the PDB in question have MODRES records in the header? These re-define the names of NAG, etc to something else that may not be handled by today's monomer library, as the different anomeric forms are now tied to the three letter code you are using (NAG -> beta-D-GlcNAc). I think it might just work if you get rid of all MODRES records in your PDB?
Let me know if that does the trick!
Best regards,
Jon
On Wed, 28 Nov 2018 at 16:24, Derek Logan <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi,
I'm trying to finish off refinement of a structure I last refined in 2009, but Refmac5 is crashing with very odd problems. I list some relevant lines from the log files below. Essentially refmac seems to think that every residue is a terminal one, as it complains that OXT is missing for every residue in the structure. It also complains that it doesn't recognise NAG residues that worked perfectly fine before. I am using the exact same coordinates that worked with Refmac5 in 2009. What can have changed?
Derek
_____________________________________________________
Derek Logan
Associate Professor, Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se<http://www.cmps.lu.se/>
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 5.51
_lib_update 11/07/18
------------------------------
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name ?
_lib_version ?
_lib_update ?
------------------------------
WARNING: duplicated name of monomer 935
Last entry will be used.
NUMBER OF MONOMERS IN THE LIBRARY : 24613
with complete description : 24613
NUMBER OF MODIFICATIONS : 71
NUMBER OF LINKS : 77
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
Number of atoms : 3107
Number of residues : 620
Number of chains : 8
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: ASP 1 chain:AAA
atom: "OXT " is absent in coord_file
WARNING : residue: THR 2 chain:AAA
atom: "OXT " is absent in coord_file
WARNING : residue: PRO 3 chain:AAA
atom: "OXT " is absent in coord_file
WARNING : residue: ALA 4 chain:AAA
atom: "OXT " is absent in coord_file
WARNING : residue: ASN 5 chain:AAA
atom: "OXT " is absent in coord_file
[and so on for every residue in the structure]
[snip]
WARNING : residue: NAG-b-D 604 chain:BaB - is not in the library
WARNING : monomer looks like 5AX ;
WARNING : the program will try to use 5AX
WARNING : residue: NAG-b-D 604 chain:BaB - rename
"NAG-b-D " --> "5AX "
[etc.]
For comparison, here is the output from 2009:
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.16
_lib_update 29/09/08
------------------------------
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name ?
_lib_version ?
_lib_update ?
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2446
with complete description : 465
NUMBER OF MODIFICATIONS : 50
NUMBER OF LINKS : 65
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
[CRYST1 line removed]
Number of atoms : 3107
Number of residues : 620
Number of chains : 8
I am reading library. Please wait.
mon_lib.cif
WARNING : residue: NAG 602 chain:Aa
atom: "O1 " is absent in coord_file
WARNING : residue: NAG 604 chain:Ba
atom: "O1 " is absent in coord_file
WARNING : residue: LEU 439 chain:CC
atom: "OXT " is absent in coord_file
and very little else
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--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz
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