May. 10, 13:01:52 2013 [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- CLOSE CONTACTS ==> Distances smaller than 2.2 Angstroms are considered as close contacts for heavy atoms, 1.6 Angstroms for hydrogens. none DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.011 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 0.6 degrees. All covalent bond angles lie within a 6.0*RMSD range about the standard dictionary values. TORSION ANGLES The torsion angle distributions have been checked. The postscript file of the conformation rings showing the torsion angle distributions will be sent in a separate E-mail message. CHIRALITY The chirality has been checked. O1P, O2P, and hydrogen atoms which do not follow the convention defined in the IUBMB (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992) and IUPAC nomenclature (J.L. Markley, A. Bax, Y. Arata, C.W. Hilbers, R. Kaptein, B.D. Sykes, P.E. Wright and K. Wüthrich, Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids, Pure & Appl. Chem., Vol. 70, pp. 117-142, 1998) have been standardized. Any other stereochemical violations are listed below. E/Z NOMENCLATURE E/Z nomenclature of hydrogens and/or nitrogens on Arg, Asn or Gln residues needs to be corrected to conform with the standard for E/Z orientation presented in [J.L. Markley, et al., Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids, Pure & Appl. Chem., 1998, 70, 117-142]. Model Chain Residue Residue Atom Name Original Name Number Atom Name ----- ----- ------- ------- -------- --------- 1 A ASN 2 1HD2 1 A ASN 2 2HD2 1 A ASN 11 1HD2 1 A ASN 11 2HD2 1 A ASN 17 1HD2 1 A ASN 17 2HD2 1 A GLN 38 1HE2 1 A GLN 38 2HE2 1 A ASN 57 1HD2 1 A ASN 57 2HD2 1 A GLN 78 1HE2 1 A GLN 78 2HE2 1 A ASN 89 1HD2 1 A ASN 89 2HD2 2 A ASN 2 1HD2 2 A ASN 2 2HD2 2 A ASN 11 1HD2 2 A ASN 11 2HD2 2 A ASN 17 1HD2 2 A ASN 17 2HD2 2 A GLN 38 1HE2 2 A GLN 38 2HE2 2 A ASN 57 1HD2 2 A ASN 57 2HD2 2 A GLN 78 1HE2 2 A GLN 78 2HE2 2 A ASN 89 1HD2 2 A ASN 89 2HD2 3 A ASN 2 1HD2 3 A ASN 2 2HD2 3 A ASN 11 1HD2 3 A ASN 11 2HD2 3 A ASN 17 1HD2 3 A ASN 17 2HD2 3 A GLN 38 1HE2 3 A GLN 38 2HE2 3 A ASN 57 1HD2 3 A ASN 57 2HD2 3 A GLN 78 1HE2 3 A GLN 78 2HE2 3 A ASN 89 1HD2 3 A ASN 89 2HD2 4 A ASN 2 1HD2 4 A ASN 2 2HD2 4 A ASN 11 1HD2 4 A ASN 11 2HD2 4 A ASN 17 1HD2 4 A ASN 17 2HD2 4 A GLN 38 1HE2 4 A GLN 38 2HE2 4 A ASN 57 1HD2 4 A ASN 57 2HD2 4 A GLN 78 1HE2 4 A GLN 78 2HE2 4 A ASN 89 1HD2 4 A ASN 89 2HD2 5 A ASN 2 1HD2 5 A ASN 2 2HD2 5 A ASN 11 1HD2 5 A ASN 11 2HD2 5 A ASN 17 1HD2 5 A ASN 17 2HD2 5 A GLN 38 1HE2 5 A GLN 38 2HE2 5 A ASN 57 1HD2 5 A ASN 57 2HD2 5 A GLN 78 1HE2 5 A GLN 78 2HE2 5 A ASN 89 1HD2 5 A ASN 89 2HD2 6 A ASN 2 1HD2 6 A ASN 2 2HD2 6 A ASN 11 1HD2 6 A ASN 11 2HD2 6 A ASN 17 1HD2 6 A ASN 17 2HD2 6 A GLN 38 1HE2 6 A GLN 38 2HE2 6 A ASN 57 1HD2 6 A ASN 57 2HD2 6 A GLN 78 1HE2 6 A GLN 78 2HE2 6 A ASN 89 1HD2 6 A ASN 89 2HD2 7 A ASN 2 1HD2 7 A ASN 2 2HD2 7 A ASN 11 1HD2 7 A ASN 11 2HD2 7 A ASN 17 1HD2 7 A ASN 17 2HD2 7 A GLN 38 1HE2 7 A GLN 38 2HE2 7 A ASN 57 1HD2 7 A ASN 57 2HD2 7 A GLN 78 1HE2 7 A GLN 78 2HE2 7 A ASN 89 1HD2 7 A ASN 89 2HD2 8 A ASN 2 1HD2 8 A ASN 2 2HD2 8 A ASN 11 1HD2 8 A ASN 11 2HD2 8 A ASN 17 1HD2 8 A ASN 17 2HD2 8 A GLN 38 1HE2 8 A GLN 38 2HE2 8 A ASN 57 1HD2 8 A ASN 57 2HD2 8 A GLN 78 1HE2 8 A GLN 78 2HE2 8 A ASN 89 1HD2 8 A ASN 89 2HD2 9 A ASN 2 1HD2 9 A ASN 2 2HD2 9 A ASN 11 1HD2 9 A ASN 11 2HD2 9 A ASN 17 1HD2 9 A ASN 17 2HD2 9 A GLN 38 1HE2 9 A GLN 38 2HE2 9 A ASN 57 1HD2 9 A ASN 57 2HD2 9 A GLN 78 1HE2 9 A GLN 78 2HE2 9 A ASN 89 1HD2 9 A ASN 89 2HD2 10 A ASN 2 1HD2 10 A ASN 2 2HD2 10 A ASN 11 1HD2 10 A ASN 11 2HD2 10 A ASN 17 1HD2 10 A ASN 17 2HD2 10 A GLN 38 1HE2 10 A GLN 38 2HE2 10 A ASN 57 1HD2 10 A ASN 57 2HD2 10 A GLN 78 1HE2 10 A GLN 78 2HE2 10 A ASN 89 1HD2 10 A ASN 89 2HD2 11 A ASN 2 1HD2 11 A ASN 2 2HD2 11 A ASN 11 1HD2 11 A ASN 11 2HD2 11 A ASN 17 1HD2 11 A ASN 17 2HD2 11 A GLN 38 1HE2 11 A GLN 38 2HE2 11 A ASN 57 1HD2 11 A ASN 57 2HD2 11 A GLN 78 1HE2 11 A GLN 78 2HE2 11 A ASN 89 1HD2 11 A ASN 89 2HD2 12 A ASN 2 1HD2 12 A ASN 2 2HD2 12 A ASN 11 1HD2 12 A ASN 11 2HD2 12 A ASN 17 1HD2 12 A ASN 17 2HD2 12 A GLN 38 1HE2 12 A GLN 38 2HE2 12 A ASN 57 1HD2 12 A ASN 57 2HD2 12 A GLN 78 1HE2 12 A GLN 78 2HE2 12 A ASN 89 1HD2 12 A ASN 89 2HD2 13 A ASN 2 1HD2 13 A ASN 2 2HD2 13 A ASN 11 1HD2 13 A ASN 11 2HD2 13 A ASN 17 1HD2 13 A ASN 17 2HD2 13 A GLN 38 1HE2 13 A GLN 38 2HE2 13 A ASN 57 1HD2 13 A ASN 57 2HD2 13 A GLN 78 1HE2 13 A GLN 78 2HE2 13 A ASN 89 1HD2 13 A ASN 89 2HD2 14 A ASN 2 1HD2 14 A ASN 2 2HD2 14 A ASN 11 1HD2 14 A ASN 11 2HD2 14 A ASN 17 1HD2 14 A ASN 17 2HD2 14 A GLN 38 1HE2 14 A GLN 38 2HE2 14 A ASN 57 1HD2 14 A ASN 57 2HD2 14 A GLN 78 1HE2 14 A GLN 78 2HE2 14 A ASN 89 1HD2 14 A ASN 89 2HD2 15 A ASN 2 1HD2 15 A ASN 2 2HD2 15 A ASN 11 1HD2 15 A ASN 11 2HD2 15 A ASN 17 1HD2 15 A ASN 17 2HD2 15 A GLN 38 1HE2 15 A GLN 38 2HE2 15 A ASN 57 1HD2 15 A ASN 57 2HD2 15 A GLN 78 1HE2 15 A GLN 78 2HE2 15 A ASN 89 1HD2 15 A ASN 89 2HD2 16 A ASN 2 1HD2 16 A ASN 2 2HD2 16 A ASN 11 1HD2 16 A ASN 11 2HD2 16 A ASN 17 1HD2 16 A ASN 17 2HD2 16 A GLN 38 1HE2 16 A GLN 38 2HE2 16 A ASN 57 1HD2 16 A ASN 57 2HD2 16 A GLN 78 1HE2 16 A GLN 78 2HE2 16 A ASN 89 1HD2 16 A ASN 89 2HD2 17 A ASN 2 1HD2 17 A ASN 2 2HD2 17 A ASN 11 1HD2 17 A ASN 11 2HD2 17 A ASN 17 1HD2 17 A ASN 17 2HD2 17 A GLN 38 1HE2 17 A GLN 38 2HE2 17 A ASN 57 1HD2 17 A ASN 57 2HD2 17 A GLN 78 1HE2 17 A GLN 78 2HE2 17 A ASN 89 1HD2 17 A ASN 89 2HD2 18 A ASN 2 1HD2 18 A ASN 2 2HD2 18 A ASN 11 1HD2 18 A ASN 11 2HD2 18 A ASN 17 1HD2 18 A ASN 17 2HD2 18 A GLN 38 1HE2 18 A GLN 38 2HE2 18 A ASN 57 1HD2 18 A ASN 57 2HD2 18 A GLN 78 1HE2 18 A GLN 78 2HE2 18 A ASN 89 1HD2 18 A ASN 89 2HD2 19 A ASN 2 1HD2 19 A ASN 2 2HD2 19 A ASN 11 1HD2 19 A ASN 11 2HD2 19 A ASN 17 1HD2 19 A ASN 17 2HD2 19 A GLN 38 1HE2 19 A GLN 38 2HE2 19 A ASN 57 1HD2 19 A ASN 57 2HD2 19 A GLN 78 1HE2 19 A GLN 78 2HE2 19 A ASN 89 1HD2 19 A ASN 89 2HD2 20 A ASN 2 1HD2 20 A ASN 2 2HD2 20 A ASN 11 1HD2 20 A ASN 11 2HD2 20 A ASN 17 1HD2 20 A ASN 17 2HD2 20 A GLN 38 1HE2 20 A GLN 38 2HE2 20 A ASN 57 1HD2 20 A ASN 57 2HD2 20 A GLN 78 1HE2 20 A GLN 78 2HE2 20 A ASN 89 1HD2 20 A ASN 89 2HD2 OTHER IMPORTANT ISSUES ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS GLU( 1 A 7) HE2 GLU( 1 A 19) HE2 GLU( 1 A 28) HE2 ASP( 1 A 33) HD2 ASP( 1 A 46) HD2 ASP( 1 A 47) HD2 GLU( 1 A 58) HE2 ASP( 1 A 61) HD2 GLU( 1 A 63) HE2 ASP( 1 A 68) HD2 GLU( 1 A 71) HE2 GLU( 1 A 84) HE2 ASP( 1 A 88) HD2 GLU( 1 A 94) HE2 GLU( 1 A 98) HE2 GLU( 2 A 7) HE2 GLU( 2 A 19) HE2 GLU( 2 A 28) HE2 ASP( 2 A 33) HD2 ASP( 2 A 46) HD2 ASP( 2 A 47) HD2 GLU( 2 A 58) HE2 ASP( 2 A 61) HD2 GLU( 2 A 63) HE2 ASP( 2 A 68) HD2 GLU( 2 A 71) HE2 GLU( 2 A 84) HE2 ASP( 2 A 88) HD2 GLU( 2 A 94) HE2 GLU( 2 A 98) HE2 GLU( 3 A 7) HE2 GLU( 3 A 19) HE2 GLU( 3 A 28) HE2 ASP( 3 A 33) HD2 ASP( 3 A 46) HD2 ASP( 3 A 47) HD2 GLU( 3 A 58) HE2 ASP( 3 A 61) HD2 GLU( 3 A 63) HE2 ASP( 3 A 68) HD2 GLU( 3 A 71) HE2 GLU( 3 A 84) HE2 ASP( 3 A 88) HD2 GLU( 3 A 94) HE2 GLU( 3 A 98) HE2 GLU( 4 A 7) HE2 GLU( 4 A 19) HE2 GLU( 4 A 28) HE2 ASP( 4 A 33) HD2 ASP( 4 A 46) HD2 ASP( 4 A 47) HD2 GLU( 4 A 58) HE2 ASP( 4 A 61) HD2 GLU( 4 A 63) HE2 ASP( 4 A 68) HD2 GLU( 4 A 71) HE2 GLU( 4 A 84) HE2 ASP( 4 A 88) HD2 GLU( 4 A 94) HE2 GLU( 4 A 98) HE2 GLU( 5 A 7) HE2 GLU( 5 A 19) HE2 GLU( 5 A 28) HE2 ASP( 5 A 33) HD2 ASP( 5 A 46) HD2 ASP( 5 A 47) HD2 GLU( 5 A 58) HE2 ASP( 5 A 61) HD2 GLU( 5 A 63) HE2 ASP( 5 A 68) HD2 GLU( 5 A 71) HE2 GLU( 5 A 84) HE2 ASP( 5 A 88) HD2 GLU( 5 A 94) HE2 GLU( 5 A 98) HE2 GLU( 6 A 7) HE2 GLU( 6 A 19) HE2 GLU( 6 A 28) HE2 ASP( 6 A 33) HD2 ASP( 6 A 46) HD2 ASP( 6 A 47) HD2 GLU( 6 A 58) HE2 ASP( 6 A 61) HD2 GLU( 6 A 63) HE2 ASP( 6 A 68) HD2 GLU( 6 A 71) HE2 GLU( 6 A 84) HE2 ASP( 6 A 88) HD2 GLU( 6 A 94) HE2 GLU( 6 A 98) HE2 GLU( 7 A 7) HE2 GLU( 7 A 19) HE2 GLU( 7 A 28) HE2 ASP( 7 A 33) HD2 ASP( 7 A 46) HD2 ASP( 7 A 47) HD2 GLU( 7 A 58) HE2 ASP( 7 A 61) HD2 GLU( 7 A 63) HE2 ASP( 7 A 68) HD2 GLU( 7 A 71) HE2 GLU( 7 A 84) HE2 ASP( 7 A 88) HD2 GLU( 7 A 94) HE2 GLU( 7 A 98) HE2 GLU( 8 A 7) HE2 GLU( 8 A 19) HE2 GLU( 8 A 28) HE2 ASP( 8 A 33) HD2 ASP( 8 A 46) HD2 ASP( 8 A 47) HD2 GLU( 8 A 58) HE2 ASP( 8 A 61) HD2 GLU( 8 A 63) HE2 ASP( 8 A 68) HD2 GLU( 8 A 71) HE2 GLU( 8 A 84) HE2 ASP( 8 A 88) HD2 GLU( 8 A 94) HE2 GLU( 8 A 98) HE2 GLU( 9 A 7) HE2 GLU( 9 A 19) HE2 GLU( 9 A 28) HE2 ASP( 9 A 33) HD2 ASP( 9 A 46) HD2 ASP( 9 A 47) HD2 GLU( 9 A 58) HE2 ASP( 9 A 61) HD2 GLU( 9 A 63) HE2 ASP( 9 A 68) HD2 GLU( 9 A 71) HE2 GLU( 9 A 84) HE2 ASP( 9 A 88) HD2 GLU( 9 A 94) HE2 GLU( 9 A 98) HE2 GLU( 10 A 7) HE2 GLU( 10 A 19) HE2 GLU( 10 A 28) HE2 ASP( 10 A 33) HD2 ASP( 10 A 46) HD2 ASP( 10 A 47) HD2 GLU( 10 A 58) HE2 ASP( 10 A 61) HD2 GLU( 10 A 63) HE2 ASP( 10 A 68) HD2 GLU( 10 A 71) HE2 GLU( 10 A 84) HE2 ASP( 10 A 88) HD2 GLU( 10 A 94) HE2 GLU( 10 A 98) HE2 GLU( 11 A 7) HE2 GLU( 11 A 19) HE2 GLU( 11 A 28) HE2 ASP( 11 A 33) HD2 ASP( 11 A 46) HD2 ASP( 11 A 47) HD2 GLU( 11 A 58) HE2 ASP( 11 A 61) HD2 GLU( 11 A 63) HE2 ASP( 11 A 68) HD2 GLU( 11 A 71) HE2 GLU( 11 A 84) HE2 ASP( 11 A 88) HD2 GLU( 11 A 94) HE2 GLU( 11 A 98) HE2 GLU( 12 A 7) HE2 GLU( 12 A 19) HE2 GLU( 12 A 28) HE2 ASP( 12 A 33) HD2 ASP( 12 A 46) HD2 ASP( 12 A 47) HD2 GLU( 12 A 58) HE2 ASP( 12 A 61) HD2 GLU( 12 A 63) HE2 ASP( 12 A 68) HD2 GLU( 12 A 71) HE2 GLU( 12 A 84) HE2 ASP( 12 A 88) HD2 GLU( 12 A 94) HE2 GLU( 12 A 98) HE2 GLU( 13 A 7) HE2 GLU( 13 A 19) HE2 GLU( 13 A 28) HE2 ASP( 13 A 33) HD2 ASP( 13 A 46) HD2 ASP( 13 A 47) HD2 GLU( 13 A 58) HE2 ASP( 13 A 61) HD2 GLU( 13 A 63) HE2 ASP( 13 A 68) HD2 GLU( 13 A 71) HE2 GLU( 13 A 84) HE2 ASP( 13 A 88) HD2 GLU( 13 A 94) HE2 GLU( 13 A 98) HE2 GLU( 14 A 7) HE2 GLU( 14 A 19) HE2 GLU( 14 A 28) HE2 ASP( 14 A 33) HD2 ASP( 14 A 46) HD2 ASP( 14 A 47) HD2 GLU( 14 A 58) HE2 ASP( 14 A 61) HD2 GLU( 14 A 63) HE2 ASP( 14 A 68) HD2 GLU( 14 A 71) HE2 GLU( 14 A 84) HE2 ASP( 14 A 88) HD2 GLU( 14 A 94) HE2 GLU( 14 A 98) HE2 GLU( 15 A 7) HE2 GLU( 15 A 19) HE2 GLU( 15 A 28) HE2 ASP( 15 A 33) HD2 ASP( 15 A 46) HD2 ASP( 15 A 47) HD2 GLU( 15 A 58) HE2 ASP( 15 A 61) HD2 GLU( 15 A 63) HE2 ASP( 15 A 68) HD2 GLU( 15 A 71) HE2 GLU( 15 A 84) HE2 ASP( 15 A 88) HD2 GLU( 15 A 94) HE2 GLU( 15 A 98) HE2 GLU( 16 A 7) HE2 GLU( 16 A 19) HE2 GLU( 16 A 28) HE2 ASP( 16 A 33) HD2 ASP( 16 A 46) HD2 ASP( 16 A 47) HD2 GLU( 16 A 58) HE2 ASP( 16 A 61) HD2 GLU( 16 A 63) HE2 ASP( 16 A 68) HD2 GLU( 16 A 71) HE2 GLU( 16 A 84) HE2 ASP( 16 A 88) HD2 GLU( 16 A 94) HE2 GLU( 16 A 98) HE2 GLU( 17 A 7) HE2 GLU( 17 A 19) HE2 GLU( 17 A 28) HE2 ASP( 17 A 33) HD2 ASP( 17 A 46) HD2 ASP( 17 A 47) HD2 GLU( 17 A 58) HE2 ASP( 17 A 61) HD2 GLU( 17 A 63) HE2 ASP( 17 A 68) HD2 GLU( 17 A 71) HE2 GLU( 17 A 84) HE2 ASP( 17 A 88) HD2 GLU( 17 A 94) HE2 GLU( 17 A 98) HE2 GLU( 18 A 7) HE2 GLU( 18 A 19) HE2 GLU( 18 A 28) HE2 ASP( 18 A 33) HD2 ASP( 18 A 46) HD2 ASP( 18 A 47) HD2 GLU( 18 A 58) HE2 ASP( 18 A 61) HD2 GLU( 18 A 63) HE2 ASP( 18 A 68) HD2 GLU( 18 A 71) HE2 GLU( 18 A 84) HE2 ASP( 18 A 88) HD2 GLU( 18 A 94) HE2 GLU( 18 A 98) HE2 GLU( 19 A 7) HE2 GLU( 19 A 19) HE2 GLU( 19 A 28) HE2 ASP( 19 A 33) HD2 ASP( 19 A 46) HD2 ASP( 19 A 47) HD2 GLU( 19 A 58) HE2 ASP( 19 A 61) HD2 GLU( 19 A 63) HE2 ASP( 19 A 68) HD2 GLU( 19 A 71) HE2 GLU( 19 A 84) HE2 ASP( 19 A 88) HD2 GLU( 19 A 94) HE2 GLU( 19 A 98) HE2 GLU( 20 A 7) HE2 GLU( 20 A 19) HE2 GLU( 20 A 28) HE2 ASP( 20 A 33) HD2 ASP( 20 A 46) HD2 ASP( 20 A 47) HD2 GLU( 20 A 58) HE2 ASP( 20 A 61) HD2 GLU( 20 A 63) HE2 ASP( 20 A 68) HD2 GLU( 20 A 71) HE2 GLU( 20 A 84) HE2 ASP( 20 A 88) HD2 GLU( 20 A 94) HE2 GLU( 20 A 98) HE2 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS GLU( 1 A 98) O2 GLU( 2 A 98) O2 GLU( 3 A 98) O2 GLU( 4 A 98) O2 GLU( 5 A 98) O2 GLU( 6 A 98) O2 GLU( 7 A 98) O2 GLU( 8 A 98) O2 GLU( 9 A 98) O2 GLU( 10 A 98) O2 GLU( 11 A 98) O2 GLU( 12 A 98) O2 GLU( 13 A 98) O2 GLU( 14 A 98) O2 GLU( 15 A 98) O2 GLU( 16 A 98) O2 GLU( 17 A 98) O2 GLU( 18 A 98) O2 GLU( 19 A 98) O2 GLU( 20 A 98) O2 MRR110B_R3Cons_em_bcr3.pdb: Missing KEYWDS records MRR110B_R3Cons_em_bcr3.pdb: Missing TITLE record