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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jaishin, You have to rename the CD atoms of your ILE residues to CD1. For some reason CNS likes to call these atoms CD, while refmac calls them CD1. You have a lot of them, so refmac produces a long list of warnings, which compel it to stop. Cheers, Miguel 劉家欣(OZ) wrote: > Dear All: > A dataset was indexed as R3 space group and subjected into CNS 1.1 > program as molecular replacement. > Fortunately, a specific solution was obtained with high c.c value. With > inspection of the pdb and density map, most part were fitted. > However, the pdb doesn't refine by refmac 5.0 module of CCP4 5.0.2 version. > A fatal error was showed and program was halted. > I have no idea about that. > Any helps would be high appreciated. > Thank you very much. > > > > jaishin > > > > --- title of input coord file --- > > PDB_code:XXXX > PDB_name:---- > PDB_date:XX-XXX-XX > -------------------------------- > WARNING : atom :CD ILE AA 7 is absent in the library > ATTENTION: atom:CD1 ILE AA 7 is missing in the structure > WARNING : atom :CD ILE AA 9 is absent in the library > ATTENTION: atom:CD1 ILE AA 9 is missing in the structure > WARNING : atom :CD ILE AA 15 is absent in the library > ATTENTION: atom:CD1 ILE AA 15 is missing in the structure > WARNING : atom :CD ILE AA 16 is absent in the library > ATTENTION: atom:CD1 ILE AA 16 is missing in the structure > WARNING : atom :CD ILE AA 31 is absent in the library > ATTENTION: atom:CD1 ILE AA 31 is missing in the structure > WARNING : atom :CD ILE AA 47 is absent in the library > ATTENTION: atom:CD1 ILE AA 47 is missing in the structure > WARNING : atom :CD ILE AA 50 is absent in the library > ATTENTION: atom:CD1 ILE AA 50 is missing in the structure > WARNING : atom :CD ILE AA 66 is absent in the library > ATTENTION: atom:CD1 ILE AA 66 is missing in the structure > WARNING : atom :CD ILE AA 74 is absent in the library > ATTENTION: atom:CD1 ILE AA 74 is missing in the structure > WARNING : atom :CD ILE AA 92 is absent in the library > ATTENTION: atom:CD1 ILE AA 92 is missing in the structure > WARNING : atom :CD ILE AA 110 is absent in the library > ATTENTION: atom:CD1 ILE AA 110 is missing in the structure > WARNING : atom :CD ILE AA 117 is absent in the library > ATTENTION: atom:CD1 ILE AA 117 is missing in the structure > WARNING : atom :CD ILE AA 149 is absent in the library > ATTENTION: atom:CD1 ILE AA 149 is missing in the structure > WARNING : atom :CD ILE AA 155 is absent in the library > ATTENTION: atom:CD1 ILE AA 155 is missing in the structure > WARNING : atom :CD ILE AA 164 is absent in the library > ATTENTION: atom:CD1 ILE AA 164 is missing in the structure > WARNING : atom :CD ILE AA 167 is absent in the library > ATTENTION: atom:CD1 ILE AA 167 is missing in the structure > WARNING : atom :CD ILE AA 173 is absent in the library > ATTENTION: atom:CD1 ILE AA 173 is missing in the structure > WARNING : atom :CD ILE AA 175 is absent in the library > ATTENTION: atom:CD1 ILE AA 175 is missing in the structure > WARNING : atom :CD ILE AA 189 is absent in the library > ATTENTION: atom:CD1 ILE AA 189 is missing in the structure > WARNING : atom :CD ILE AA 196 is absent in the library > ... and more ... > ATTENTION: atom:CD1 ILE AA 196 is missing in the structure > ... and more ... > > Spacegroup information obtained from library file: > Logical Name: SYMINFO Filename: C:\CCP4win5.0.2\lib\data\syminfo.lib > > End of this subr > Number of chains : 2 > Total number of monomers : 696 > Number of atoms : 5402 > Number of missing atoms : 66 > Number of rebuilt atoms : 0 > Number of unknown atoms : 66 > Number of deleted atoms : 0 > > Number of bonds restraints : 5360 > Number of angles restraints : 7282 > Number of torsions restraints : 3606 > Number of chiralities : 870 > Number of planar groups : 928 > IERR = 1 > > There is error. See above > ===> Error: Fatal error. Cannot continue > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > Refmac_5.2.0005: Fatal error. Cannot continue > Times: User: 0.0s System: 0.0s Elapsed: 0:17 > </pre> > </html> > <!--SUMMARY_END--> - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFERzqLF6oOrDvhbQIRAleWAJwIWS8TBsBy2V27LeRgFzlbnx7uUgCfYCW3 mV5BtXNqryqDrwC6Fg4/9RY= =beeM -----END PGP SIGNATURE-----
