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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
