May. 10, 06:12:05 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 1.2 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 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 PRO( A -77 ) PRO( A -76 ) PRO( A -75 ) ASN( A -74 ) GLU( A -73 ) GLU( A -72 ) ALA( A -71 ) ARG( A -70 ) LEU( A -69 ) ASP( A -68 ) ILE( A -67 ) LEU( A -66 ) LYS( A -65 ) ILE( A -64 ) HIS( A -63 ) SER( A -62 ) ARG( A -61 ) LYS( A -60 ) MSE( A -59 ) ASN( A -58 ) LEU( A -57 ) THR( A -56 ) ARG( A -55 ) GLY( A -54 ) ILE( A -53 ) ASN( A -52 ) LEU( A -51 ) ARG( A -50 ) LYS( A -49 ) ILE( A -48 ) ALA( A -47 ) GLU( A -46 ) LEU( A -45 ) MSE( A -44 ) PRO( A -43 ) GLY( A -42 ) ALA( A -41 ) SER( A -40 ) GLY( A -39 ) ALA( A -38 ) GLU( A -37 ) VAL( A -36 ) LYS( A -35 ) GLY( A -34 ) VAL( A -33 ) CYS( A -32 ) THR( A -31 ) GLU( A -30 ) ALA( A -29 ) GLY( A -28 ) MSE( A -27 ) TYR( A -26 ) ALA( A -25 ) LEU( A -24 ) ARG( A -23 ) GLU( A -22 ) ARG( A -21 ) ARG( A -20 ) VAL( A -19 ) HIS( A -18 ) VAL( A -17 ) THR( A -16 ) GLN( A -15 ) GLU( A -14 ) ASP( A -13 ) PHE( A -12 ) GLU( A -11 ) MSE( A -10 ) ALA( A -9 ) VAL( A -8 ) ALA( A -7 ) LYS( A -6 ) VAL( A -5 ) MSE( A -4 ) GLN( A -3 ) LYS( A -2 ) ASP( A -1 ) SER( A 0 ) PDB Chain_ID: A 1 15 SEQRES: PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU LYS ILE HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU ARG LYS ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL LYS GLY VAL COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG ARG VAL HIS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS VAL MSE GLN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: LYS ASP SER PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU COORDS: ... ... ... PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU 1 12 91 105 SEQRES: LYS ILE HIS SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU COORDS: LYS ILE HIS SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU 13 27 106 120 SEQRES: ARG LYS ILE ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL COORDS: ARG LYS ILE ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL 28 42 121 135 SEQRES: LYS GLY VAL CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG COORDS: LYS GLY VAL CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG 43 57 136 150 SEQRES: ARG VAL HIS VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS COORDS: ARG VAL HIS VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS 58 72 151 153 SEQRES: VAL MSE GLN COORDS: VAL MSE GLN 73 75 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS PRO( A 1) CG CD PRO( A 2) CG CD GLN( A 75) CG CD OE1 NE2 HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 2) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ARG CHNID: A SSEQ: 15) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 24) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: LEU CHNID: A SSEQ: 31) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: SER CHNID: A SSEQ: 36) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: GLU CHNID: A SSEQ: 54) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: THR CHNID: A SSEQ: 60) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: GLN CHNID: A SSEQ: 73) in Token 'HELIX' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 17) in Token 'MODRES' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 32) in Token 'MODRES' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 49) in Token 'MODRES' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 66) in Token 'MODRES' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 72) in Token 'MODRES' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 18) in Token 'SHEET' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: LEU CHNID: A SSEQ: 19) in Token 'SHEET' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: HIS CHNID: A SSEQ: 58) in Token 'SHEET' can not be found in coordinates HR3102A_XRay_em_bcr3.pdb: Error: Record (ATOM: N RES: ASN CHNID: A SSEQ: 18) in Token 'SHEET' can not be found in coordinates