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
------------------------------
--- 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