May. 14, 15:08:42 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 The following table contains a list of the covalent bonds greater than 6.0*RMSD. Deviation Residue Chain Sequence Model AT1 - AT2 Bond Dictionary Name ID Number Distance Value ------------------------------------------------------------------------ 0.069 PRO A 76 8 CD - N 1.542 1.473 *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 0.6 degrees. The following table contains a list of the covalent bond angles greater than 6.0*RMSD. Deviation Residue Chain Sequence Model AT1 - AT2 - AT3 Bond Dictionary Name ID Number Angle Value -------------------------------------------------------------------------------- -4.5 TYR A 31 1 CA - CB - CG 109.4 113.9 -6.7 LEU A 46 2 CA - CB - CG 109.6 116.3 -4.4 TRP A 71 2 CA - CB - CG 109.2 113.6 -4.1 PHE A 82 2 CA - CB - CG 109.7 113.8 -4.4 TRP A 71 3 CA - CB - CG 109.2 113.6 -4.0 PHE A 82 3 CA - CB - CG 109.8 113.8 -6.5 LEU A 19 4 CA - CB - CG 109.8 116.3 -4.2 PHE A 82 4 CA - CB - CG 109.6 113.8 -3.9 TRP A 71 5 CA - CB - CG 109.7 113.6 -4.8 HIS A 12 6 CA - CB - CG 109.0 113.8 -3.9 HIS A 12 6 CE1 - NE2 - CD2 105.1 109.0 -3.9 GLN A 38 6 CA - CB - CG 110.2 114.1 -4.2 TRP A 71 6 CA - CB - CG 109.4 113.6 -5.4 PHE A 82 6 CA - CB - CG 108.4 113.8 -4.1 TYR A 31 7 CA - CB - CG 109.8 113.9 -4.0 TRP A 71 7 CA - CB - CG 109.6 113.6 -3.9 PHE A 82 7 CA - CB - CG 109.9 113.8 -4.1 TRP A 71 8 CA - CB - CG 109.5 113.6 -4.4 PHE A 82 9 CA - CB - CG 109.4 113.8 -4.1 TYR A 31 10 CA - CB - CG 109.8 113.9 -4.5 PHE A 82 10 CA - CB - CG 109.3 113.8 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 11 1HD2 1 A ASN 11 2HD2 1 A ASN 13 1HD2 1 A ASN 13 2HD2 1 A GLN 38 1HE2 1 A GLN 38 2HE2 1 A ASN 43 1HD2 1 A ASN 43 2HD2 1 A ASN 67 1HD2 1 A ASN 67 2HD2 1 A ASN 70 1HD2 1 A ASN 70 2HD2 2 A ASN 11 1HD2 2 A ASN 11 2HD2 2 A ASN 13 1HD2 2 A ASN 13 2HD2 2 A GLN 38 1HE2 2 A GLN 38 2HE2 2 A ASN 43 1HD2 2 A ASN 43 2HD2 2 A ASN 67 1HD2 2 A ASN 67 2HD2 2 A ASN 70 1HD2 2 A ASN 70 2HD2 3 A ASN 11 1HD2 3 A ASN 11 2HD2 3 A ASN 13 1HD2 3 A ASN 13 2HD2 3 A GLN 38 1HE2 3 A GLN 38 2HE2 3 A ASN 43 1HD2 3 A ASN 43 2HD2 3 A ASN 67 1HD2 3 A ASN 67 2HD2 3 A ASN 70 1HD2 3 A ASN 70 2HD2 4 A ASN 11 1HD2 4 A ASN 11 2HD2 4 A ASN 13 1HD2 4 A ASN 13 2HD2 4 A GLN 38 1HE2 4 A GLN 38 2HE2 4 A ASN 43 1HD2 4 A ASN 43 2HD2 4 A ASN 67 1HD2 4 A ASN 67 2HD2 4 A ASN 70 1HD2 4 A ASN 70 2HD2 5 A ASN 11 1HD2 5 A ASN 11 2HD2 5 A ASN 13 1HD2 5 A ASN 13 2HD2 5 A GLN 38 1HE2 5 A GLN 38 2HE2 5 A ASN 43 1HD2 5 A ASN 43 2HD2 5 A ASN 67 1HD2 5 A ASN 67 2HD2 5 A ASN 70 1HD2 5 A ASN 70 2HD2 6 A ASN 11 1HD2 6 A ASN 11 2HD2 6 A ASN 13 1HD2 6 A ASN 13 2HD2 6 A GLN 38 1HE2 6 A GLN 38 2HE2 6 A ASN 43 1HD2 6 A ASN 43 2HD2 6 A ASN 67 1HD2 6 A ASN 67 2HD2 6 A ASN 70 1HD2 6 A ASN 70 2HD2 7 A ASN 11 1HD2 7 A ASN 11 2HD2 7 A ASN 13 1HD2 7 A ASN 13 2HD2 7 A GLN 38 1HE2 7 A GLN 38 2HE2 7 A ASN 43 1HD2 7 A ASN 43 2HD2 7 A ASN 67 1HD2 7 A ASN 67 2HD2 7 A ASN 70 1HD2 7 A ASN 70 2HD2 8 A ASN 11 1HD2 8 A ASN 11 2HD2 8 A ASN 13 1HD2 8 A ASN 13 2HD2 8 A GLN 38 1HE2 8 A GLN 38 2HE2 8 A ASN 43 1HD2 8 A ASN 43 2HD2 8 A ASN 67 1HD2 8 A ASN 67 2HD2 8 A ASN 70 1HD2 8 A ASN 70 2HD2 9 A ASN 11 1HD2 9 A ASN 11 2HD2 9 A ASN 13 1HD2 9 A ASN 13 2HD2 9 A GLN 38 1HE2 9 A GLN 38 2HE2 9 A ASN 43 1HD2 9 A ASN 43 2HD2 9 A ASN 67 1HD2 9 A ASN 67 2HD2 9 A ASN 70 1HD2 9 A ASN 70 2HD2 10 A ASN 11 1HD2 10 A ASN 11 2HD2 10 A ASN 13 1HD2 10 A ASN 13 2HD2 10 A GLN 38 1HE2 10 A GLN 38 2HE2 10 A ASN 43 1HD2 10 A ASN 43 2HD2 10 A ASN 67 1HD2 10 A ASN 67 2HD2 10 A ASN 70 1HD2 10 A ASN 70 2HD2 OTHER IMPORTANT ISSUES ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS GLU( 1 A 8) HE2 HIS( 1 A 12) HE2 GLU( 1 A 21) HE2 GLU( 1 A 24) HE2 ASP( 1 A 29) HD2 ASP( 1 A 35) HD2 ASP( 1 A 36) HD2 ASP( 1 A 44) HD2 GLU( 1 A 49) HE2 HIS( 1 A 56) HE2 ASP( 1 A 59) HD2 ASP( 1 A 64) HD2 GLU( 1 A 66) HE2 ASP( 1 A 68) HD2 GLU( 1 A 72) HE2 GLU( 1 A 79) HE2 GLU( 1 A 83) HE2 GLU( 1 A 85) HE2 HIS( 1 A 86) HD1 HIS( 1 A 87) HE2 HIS( 1 A 88) HD1 HIS( 1 A 89) HE2 HIS( 1 A 90) HD1 HIS( 1 A 91) HE2 GLU( 2 A 8) HE2 HIS( 2 A 12) HE2 GLU( 2 A 21) HE2 GLU( 2 A 24) HE2 ASP( 2 A 29) HD2 ASP( 2 A 35) HD2 ASP( 2 A 36) HD2 ASP( 2 A 44) HD2 GLU( 2 A 49) HE2 HIS( 2 A 56) HE2 ASP( 2 A 59) HD2 ASP( 2 A 64) HD2 GLU( 2 A 66) HE2 ASP( 2 A 68) HD2 GLU( 2 A 72) HE2 GLU( 2 A 79) HE2 GLU( 2 A 83) HE2 GLU( 2 A 85) HE2 HIS( 2 A 86) HE2 HIS( 2 A 87) HD1 HIS( 2 A 88) HD1 HIS( 2 A 89) HD1 HIS( 2 A 90) HE2 HIS( 2 A 91) HE2 GLU( 3 A 8) HE2 HIS( 3 A 12) HE2 GLU( 3 A 21) HE2 GLU( 3 A 24) HE2 ASP( 3 A 29) HD2 ASP( 3 A 35) HD2 ASP( 3 A 36) HD2 ASP( 3 A 44) HD2 GLU( 3 A 49) HE2 HIS( 3 A 56) HE2 ASP( 3 A 59) HD2 ASP( 3 A 64) HD2 GLU( 3 A 66) HE2 ASP( 3 A 68) HD2 GLU( 3 A 72) HE2 GLU( 3 A 79) HE2 GLU( 3 A 83) HE2 GLU( 3 A 85) HE2 HIS( 3 A 86) HD1 HIS( 3 A 87) HD1 HIS( 3 A 88) HD1 HIS( 3 A 89) HE2 HIS( 3 A 90) HE2 HIS( 3 A 91) HD1 GLU( 4 A 8) HE2 HIS( 4 A 12) HE2 GLU( 4 A 21) HE2 GLU( 4 A 24) HE2 ASP( 4 A 29) HD2 ASP( 4 A 35) HD2 ASP( 4 A 36) HD2 ASP( 4 A 44) HD2 GLU( 4 A 49) HE2 HIS( 4 A 56) HE2 ASP( 4 A 59) HD2 ASP( 4 A 64) HD2 GLU( 4 A 66) HE2 ASP( 4 A 68) HD2 GLU( 4 A 72) HE2 GLU( 4 A 79) HE2 GLU( 4 A 83) HE2 GLU( 4 A 85) HE2 HIS( 4 A 86) HD1 HIS( 4 A 87) HE2 HIS( 4 A 88) HD1 HIS( 4 A 89) HD1 HIS( 4 A 90) HE2 HIS( 4 A 91) HD1 GLU( 5 A 8) HE2 HIS( 5 A 12) HE2 GLU( 5 A 21) HE2 GLU( 5 A 24) HE2 ASP( 5 A 29) HD2 ASP( 5 A 35) HD2 ASP( 5 A 36) HD2 ASP( 5 A 44) HD2 GLU( 5 A 49) HE2 HIS( 5 A 56) HE2 ASP( 5 A 59) HD2 ASP( 5 A 64) HD2 GLU( 5 A 66) HE2 ASP( 5 A 68) HD2 GLU( 5 A 72) HE2 GLU( 5 A 79) HE2 GLU( 5 A 83) HE2 GLU( 5 A 85) HE2 HIS( 5 A 86) HE2 HIS( 5 A 87) HE2 HIS( 5 A 88) HE2 HIS( 5 A 89) HE2 HIS( 5 A 90) HE2 HIS( 5 A 91) HD1 GLU( 6 A 8) HE2 HIS( 6 A 12) HE2 GLU( 6 A 21) HE2 GLU( 6 A 24) HE2 ASP( 6 A 29) HD2 ASP( 6 A 35) HD2 ASP( 6 A 36) HD2 ASP( 6 A 44) HD2 GLU( 6 A 49) HE2 HIS( 6 A 56) HE2 ASP( 6 A 59) HD2 ASP( 6 A 64) HD2 GLU( 6 A 66) HE2 ASP( 6 A 68) HD2 GLU( 6 A 72) HE2 GLU( 6 A 79) HE2 GLU( 6 A 83) HE2 GLU( 6 A 85) HE2 HIS( 6 A 86) HE2 HIS( 6 A 87) HD1 HIS( 6 A 88) HE2 HIS( 6 A 89) HE2 HIS( 6 A 90) HE2 HIS( 6 A 91) HD1 GLU( 7 A 8) HE2 HIS( 7 A 12) HE2 GLU( 7 A 21) HE2 GLU( 7 A 24) HE2 ASP( 7 A 29) HD2 ASP( 7 A 35) HD2 ASP( 7 A 36) HD2 ASP( 7 A 44) HD2 GLU( 7 A 49) HE2 HIS( 7 A 56) HE2 ASP( 7 A 59) HD2 ASP( 7 A 64) HD2 GLU( 7 A 66) HE2 ASP( 7 A 68) HD2 GLU( 7 A 72) HE2 GLU( 7 A 79) HE2 GLU( 7 A 83) HE2 GLU( 7 A 85) HE2 HIS( 7 A 86) HD1 HIS( 7 A 87) HD1 HIS( 7 A 88) HE2 HIS( 7 A 89) HD1 HIS( 7 A 90) HD1 HIS( 7 A 91) HE2 GLU( 8 A 8) HE2 HIS( 8 A 12) HE2 GLU( 8 A 21) HE2 GLU( 8 A 24) HE2 ASP( 8 A 29) HD2 ASP( 8 A 35) HD2 ASP( 8 A 36) HD2 ASP( 8 A 44) HD2 GLU( 8 A 49) HE2 HIS( 8 A 56) HE2 ASP( 8 A 59) HD2 ASP( 8 A 64) HD2 GLU( 8 A 66) HE2 ASP( 8 A 68) HD2 GLU( 8 A 72) HE2 GLU( 8 A 79) HE2 GLU( 8 A 83) HE2 GLU( 8 A 85) HE2 HIS( 8 A 86) HE2 HIS( 8 A 87) HE2 HIS( 8 A 88) HD1 HIS( 8 A 89) HE2 HIS( 8 A 90) HD1 HIS( 8 A 91) HD1 GLU( 9 A 8) HE2 HIS( 9 A 12) HE2 GLU( 9 A 21) HE2 GLU( 9 A 24) HE2 ASP( 9 A 29) HD2 ASP( 9 A 35) HD2 ASP( 9 A 36) HD2 ASP( 9 A 44) HD2 GLU( 9 A 49) HE2 HIS( 9 A 56) HE2 ASP( 9 A 59) HD2 ASP( 9 A 64) HD2 GLU( 9 A 66) HE2 ASP( 9 A 68) HD2 GLU( 9 A 72) HE2 GLU( 9 A 79) HE2 GLU( 9 A 83) HE2 GLU( 9 A 85) HE2 HIS( 9 A 86) HE2 HIS( 9 A 87) HD1 HIS( 9 A 88) HE2 HIS( 9 A 89) HD1 HIS( 9 A 90) HE2 HIS( 9 A 91) HE2 GLU( 10 A 8) HE2 HIS( 10 A 12) HE2 GLU( 10 A 21) HE2 GLU( 10 A 24) HE2 ASP( 10 A 29) HD2 ASP( 10 A 35) HD2 ASP( 10 A 36) HD2 ASP( 10 A 44) HD2 GLU( 10 A 49) HE2 HIS( 10 A 56) HE2 ASP( 10 A 59) HD2 ASP( 10 A 64) HD2 GLU( 10 A 66) HE2 ASP( 10 A 68) HD2 GLU( 10 A 72) HE2 GLU( 10 A 79) HE2 GLU( 10 A 83) HE2 GLU( 10 A 85) HE2 HIS( 10 A 86) HE2 HIS( 10 A 87) HE2 HIS( 10 A 88) HD1 HIS( 10 A 89) HD1 HIS( 10 A 90) HD1 HIS( 10 A 91) HD1 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS HIS( 1 A 91) O2 HIS( 2 A 91) O2 HIS( 3 A 91) O2 HIS( 4 A 91) O2 HIS( 5 A 91) O2 HIS( 6 A 91) O2 HIS( 7 A 91) O2 HIS( 8 A 91) O2 HIS( 9 A 91) O2 HIS( 10 A 91) O2 ZR18_R3Cons_em_bcr3.pdb: Missing KEYWDS records ZR18_R3Cons_em_bcr3.pdb: Missing TITLE record