May. 10, 13:29:58 2013 Greetings, [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> The following solvent molecules are further away than 3.5 Angstroms from macromolecule atoms which are available for hydrogen bonding in the asymmetric unit. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: none ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> 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 0.005 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 1.4 degrees. The following table contains a list of the covalent bond angles greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Name ID Number Angle Value -------------------------------------------------------------------------------- -11.6 LYS A 3 N - CA - C 99.6 111.2 -9.3 ASN A 16 N - CA - C 101.9 111.2 -9.1 PHE A 42 N - CA - C 102.1 111.2 -8.7 ILE A 68 N - CA - C 102.5 111.2 -8.9 GLU A 70 N - CA - C 102.3 111.2 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 and there are no incorrect carbon chiral centers. Some of O1P and O2P atoms do not follow the convention defined in the standard IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not indicate otherwise, we will switch the labels of O1P and O2P as shown below. OTHER IMPORTANT ISSUES ==> Please check carefully REMARKS 3 and 200 and fill in the parameters as appropriate. ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ MSE( A -97 ) ASN( A -96 ) TYR( A -95 ) LYS( A -94 ) ILE( A -93 ) SER( A -92 ) GLU( A -91 ) LEU( A -90 ) MSE( A -89 ) PRO( A -88 ) ASN( A -87 ) LEU( A -86 ) SER( A -85 ) GLY( A -84 ) THR( A -83 ) ILE( A -82 ) ASN( A -81 ) ALA( A -80 ) GLU( A -79 ) VAL( A -78 ) VAL( A -77 ) THR( A -76 ) ALA( A -75 ) TYR( A -74 ) PRO( A -73 ) LYS( A -72 ) LYS( A -71 ) GLU( A -70 ) PHE( A -69 ) SER( A -68 ) ARG( A -67 ) LYS( A -66 ) ASP( A -65 ) GLY( A -64 ) THR( A -63 ) LYS( A -62 ) GLY( A -61 ) GLN( A -60 ) LEU( A -59 ) LYS( A -58 ) SER( A -57 ) LEU( A -56 ) PHE( A -55 ) LEU( A -54 ) LYS( A -53 ) ASP( A -52 ) ASP( A -51 ) THR( A -50 ) GLY( A -49 ) SER( A -48 ) ILE( A -47 ) ARG( A -46 ) GLY( A -45 ) THR( A -44 ) LEU( A -43 ) TRP( A -42 ) ASN( A -41 ) GLU( A -40 ) LEU( A -39 ) ALA( A -38 ) ASP( A -37 ) PHE( A -36 ) GLU( A -35 ) VAL( A -34 ) LYS( A -33 ) LYS( A -32 ) GLY( A -31 ) ASP( A -30 ) ILE( A -29 ) ALA( A -28 ) GLU( A -27 ) VAL( A -26 ) SER( A -25 ) GLY( A -24 ) TYR( A -23 ) VAL( A -22 ) LYS( A -21 ) GLN( A -20 ) GLY( A -19 ) TYR( A -18 ) SER( A -17 ) GLY( A -16 ) LEU( A -15 ) GLU( A -14 ) ILE( A -13 ) SER( A -12 ) VAL( A -11 ) ASP( A -10 ) ASN( A -9 ) ILE( A -8 ) GLY( A -7 ) ILE( A -6 ) ILE( A -5 ) GLU( A -4 ) LYS( A -3 ) SER( A -2 ) LEU( A -1 ) SEQUENCE WARNING: Residue (A SER 29 ) and Residue (A THR 34 ) are not linked Distance of C-N bond is 5.87 SEQUENCE WARNING: Residue (A GLY 78 ) and Residue (A GLY 81 ) are not linked Distance of C-N bond is 4.96 PDB Chain_ID: A 1 15 SEQRES: MSE ASN TYR LYS ILE SER GLU LEU MSE PRO ASN LEU SER GLY THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ILE ASN ALA GLU VAL VAL THR ALA TYR PRO LYS LYS GLU PHE SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: ARG LYS ASP GLY THR LYS GLY GLN LEU LYS SER LEU PHE LEU LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN GLU LEU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL SER GLY TYR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: VAL LYS GLN GLY TYR SER GLY LEU GLU ILE SER VAL ASP ASN ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: GLY ILE ILE GLU LYS SER LEU MSE ASN TYR LYS ILE SER GLU LEU COORDS: ... ... ... ... ... ... ... MSE ASN TYR LYS ILE SER GLU LEU 0 7 106 120 SEQRES: MSE PRO ASN LEU SER GLY THR ILE ASN ALA GLU VAL VAL THR ALA COORDS: MSE PRO ASN LEU SER GLY THR ILE ASN ALA GLU VAL VAL THR ALA 8 22 121 135 SEQRES: TYR PRO LYS LYS GLU PHE SER THR LYS GLY GLN LEU LYS SER LEU COORDS: TYR PRO LYS LYS GLU PHE SER THR LYS GLY GLN LEU LYS SER LEU 23 41 136 150 SEQRES: PHE LEU LYS ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN COORDS: PHE LEU LYS ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN 42 56 151 165 SEQRES: GLU LEU ALA ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL COORDS: GLU LEU ALA ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL 57 71 166 180 SEQRES: SER GLY TYR VAL LYS GLN GLY GLY LEU GLU ILE SER VAL ASP ASN COORDS: SER GLY TYR VAL LYS GLN GLY GLY LEU GLU ILE SER VAL ASP ASN 72 88 181 188 SEQRES: ILE GLY ILE ILE GLU LYS SER LEU COORDS: ILE GLY ILE ILE GLU LYS SER LEU 89 96 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS THR( A 34) OG1 CG2 LYS( A 35) CB CG CD CE NZ LYS( A 76) CG CD CE NZ GLN( A 77) CG CD OE1 NE2 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS LEU( A 96) O2