May. 9, 23:54:49 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 0.006 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 -------------------------------------------------------------------------------- -11.1 LEU A 20 N - CA - C 100.1 111.2 -10.5 ILE A 22 N - CA - C 100.7 111.2 -9.8 PRO A 76 N - CA - C 102.0 111.8 -9.4 THR A 92 N - CA - C 101.8 111.2 -9.8 ALA A 98 N - CA - C 101.4 111.2 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-152 ) ASP( A-151 ) PHE( A-150 ) GLU( A-149 ) CYS( A-148 ) GLN( A-147 ) PHE( A-146 ) VAL( A-145 ) CYS( A-144 ) GLU( A-143 ) LEU( A-142 ) LYS( A-141 ) GLU( A-140 ) LEU( A-139 ) ALA( A-138 ) PRO( A-137 ) VAL( A-136 ) PRO( A-135 ) ALA( A-134 ) LEU( A-133 ) LEU( A-132 ) ILE( A-131 ) ARG( A-130 ) THR( A-129 ) GLN( A-128 ) THR( A-127 ) THR( A-126 ) MSE( A-125 ) SER( A-124 ) GLU( A-123 ) LEU( A-122 ) GLY( A-121 ) SER( A-120 ) LEU( A-119 ) PHE( A-118 ) GLU( A-117 ) ALA( A-116 ) GLY( A-115 ) TYR( A-114 ) HIS( A-113 ) ASP( A-112 ) ILE( A-111 ) LEU( A-110 ) GLN( A-109 ) LEU( A-108 ) LEU( A-107 ) ALA( A-106 ) GLY( A-105 ) GLN( A-104 ) GLY( A-103 ) LYS( A-102 ) SER( A-101 ) PRO( A-100 ) SER( A -99 ) GLY( A -98 ) PRO( A -97 ) PRO( A -96 ) PHE( A -95 ) ALA( A -94 ) ARG( A -93 ) TYR( A -92 ) PHE( A -91 ) GLY( A -90 ) MSE( A -89 ) SER( A -88 ) ALA( A -87 ) GLY( A -86 ) THR( A -85 ) PHE( A -84 ) GLU( A -83 ) VAL( A -82 ) GLU( A -81 ) PHE( A -80 ) GLY( A -79 ) PHE( A -78 ) PRO( A -77 ) VAL( A -76 ) GLU( A -75 ) GLY( A -74 ) GLY( A -73 ) VAL( A -72 ) GLU( A -71 ) GLY( A -70 ) SER( A -69 ) GLY( A -68 ) ARG( A -67 ) VAL( A -66 ) VAL( A -65 ) THR( A -64 ) GLY( A -63 ) LEU( A -62 ) THR( A -61 ) PRO( A -60 ) SER( A -59 ) GLY( A -58 ) LYS( A -57 ) ALA( A -56 ) ALA( A -55 ) SER( A -54 ) SER( A -53 ) LEU( A -52 ) TYR( A -51 ) ILE( A -50 ) GLY( A -49 ) PRO( A -48 ) TYR( A -47 ) GLY( A -46 ) GLU( A -45 ) ILE( A -44 ) GLU( A -43 ) ALA( A -42 ) VAL( A -41 ) TYR( A -40 ) ASP( A -39 ) ALA( A -38 ) LEU( A -37 ) MSE( A -36 ) LYS( A -35 ) TRP( A -34 ) VAL( A -33 ) ASP( A -32 ) ASP( A -31 ) ASN( A -30 ) GLY( A -29 ) PHE( A -28 ) ASP( A -27 ) LEU( A -26 ) SER( A -25 ) GLY( A -24 ) GLU( A -23 ) ALA( A -22 ) TYR( A -21 ) GLU( A -20 ) ILE( A -19 ) TYR( A -18 ) LEU( A -17 ) ASP( A -16 ) ASN( A -15 ) PRO( A -14 ) ALA( A -13 ) GLU( A -12 ) THR( A -11 ) ALA( A -10 ) PRO( A -9 ) ASP( A -8 ) GLN( A -7 ) LEU( A -6 ) ARG( A -5 ) THR( A -4 ) ARG( A -3 ) VAL( A -2 ) SER( A -1 ) LEU( A 0 ) MSE( A 1 ) LEU( A 2 ) HIS( A 3 ) GLU( A 4 ) SER( A 5 ) PDB Chain_ID: A 1 15 SEQRES: MSE ASP PHE GLU CYS GLN PHE VAL CYS GLU LEU LYS GLU LEU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: PRO VAL PRO ALA LEU LEU ILE ARG THR GLN THR THR MSE SER GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: LEU GLY SER LEU PHE GLU ALA GLY TYR HIS ASP ILE LEU GLN LEU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: LEU ALA GLY GLN GLY LYS SER PRO SER GLY PRO PRO PHE ALA ARG COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: TYR PHE GLY MSE SER ALA GLY THR PHE GLU VAL GLU PHE GLY PHE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: PRO VAL GLU GLY GLY VAL GLU GLY SER GLY ARG VAL VAL THR GLY COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: LEU THR PRO SER GLY LYS ALA ALA SER SER LEU TYR ILE GLY PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: TYR GLY GLU ILE GLU ALA VAL TYR ASP ALA LEU MSE LYS TRP VAL COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 121 135 SEQRES: ASP ASP ASN GLY PHE ASP LEU SER GLY GLU ALA TYR GLU ILE TYR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 136 150 SEQRES: LEU ASP ASN PRO ALA GLU THR ALA PRO ASP GLN LEU ARG THR ARG COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 151 165 SEQRES: VAL SER LEU MSE LEU HIS GLU SER GLN PHE VAL CYS GLU LEU LYS COORDS: ... ... ... ... ... ... ... ... GLN PHE VAL CYS GLU LEU LYS 6 12 166 180 SEQRES: GLU LEU ALA PRO VAL PRO ALA LEU LEU ILE ARG THR GLN THR THR COORDS: GLU LEU ALA PRO VAL PRO ALA LEU LEU ILE ARG THR GLN THR THR 13 27 181 195 SEQRES: MET SER GLU LEU GLY SER LEU PHE GLU ALA GLY TYR HIS ASP ILE COORDS: MET SER GLU LEU GLY SER LEU PHE GLU ALA GLY TYR HIS ASP ILE 28 42 196 210 SEQRES: LEU GLN LEU LEU ALA GLY GLN GLY LYS SER PRO SER GLY PRO PRO COORDS: LEU GLN LEU LEU ALA GLY GLN GLY LYS SER PRO SER GLY PRO PRO 43 57 211 225 SEQRES: PHE ALA ARG TYR PHE GLY MET SER ALA GLY THR PHE GLU VAL GLU COORDS: PHE ALA ARG TYR PHE GLY MET SER ALA GLY THR PHE GLU VAL GLU 58 72 226 240 SEQRES: PHE GLY PHE PRO VAL GLU GLY GLY VAL GLU GLY SER GLY ARG VAL COORDS: PHE GLY PHE PRO VAL GLU GLY GLY VAL GLU GLY SER GLY ARG VAL 73 87 241 255 SEQRES: VAL THR GLY LEU THR PRO SER GLY LYS ALA ALA SER SER LEU TYR COORDS: VAL THR GLY LEU THR PRO SER GLY LYS ALA ALA SER SER LEU TYR 88 102 256 270 SEQRES: ILE GLY PRO TYR GLY GLU ILE GLU ALA VAL TYR ASP ALA LEU MET COORDS: ILE GLY PRO TYR GLY GLU ILE GLU ALA VAL TYR ASP ALA LEU MET 103 117 271 285 SEQRES: LYS TRP VAL ASP ASP ASN GLY PHE ASP LEU SER GLY GLU ALA TYR COORDS: LYS TRP VAL ASP ASP ASN GLY PHE ASP LEU SER GLY GLU ALA TYR 118 132 286 300 SEQRES: GLU ILE TYR LEU ASP ASN PRO ALA GLU THR ALA PRO ASP GLN LEU COORDS: GLU ILE TYR LEU ASP ASN PRO ALA GLU THR ALA PRO ASP GLN LEU 133 147 301 311 SEQRES: ARG THR ARG VAL SER LEU MET LEU HIS GLU SER COORDS: ARG THR ARG VAL SER LEU MET LEU HIS GLU SER 148 158 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS MET( A 28) SD MET( A 64) SD MET( A 117) SD MET( A 154) SD ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS MET( A 28) SE MET( A 64) SE MET( A 117) SE MET( A 154) SE SER( A 158) O2 CTR107_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 28) in Token 'MODRES' can not be found in coordinates CTR107_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 64) in Token 'MODRES' can not be found in coordinates CTR107_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 117) in Token 'MODRES' can not be found in coordinates CTR107_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 154) in Token 'MODRES' can not be found in coordinates