May. 9, 21:28:43 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 0.009 Angstroms The following table contains a list of the covalent bonds greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 Bond Dictionary Name ID Number Distance Value ------------------------------------------------------------------------ -0.061 VAL A 46 CA - C 1.464 1.525 *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.7 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 MSE( A-143 ) LYS( A-142 ) LEU( A-141 ) HIS( A-140 ) THR( A-139 ) ASP( A-138 ) PRO( A-137 ) ALA( A-136 ) THR( A-135 ) ALA( A-134 ) LEU( A-133 ) ASN( A-132 ) THR( A-131 ) VAL( A-130 ) THR( A-129 ) ALA( A-128 ) TYR( A-127 ) GLY( A-126 ) ASP( A-125 ) GLY( A-124 ) TYR( A-123 ) ILE( A-122 ) GLU( A-121 ) VAL( A-120 ) ASN( A-119 ) GLN( A-118 ) VAL( A-117 ) ARG( A-116 ) PHE( A-115 ) SER( A-114 ) HIS( A-113 ) ALA( A-112 ) ILE( A-111 ) ALA( A-110 ) PHE( A-109 ) ALA( A-108 ) PRO( A-107 ) GLU( A-106 ) GLY( A-105 ) PRO( A-104 ) VAL( A-103 ) ALA( A-102 ) SER( A-101 ) TRP( A-100 ) PRO( A -99 ) VAL( A -98 ) GLN( A -97 ) ARG( A -96 ) PRO( A -95 ) ALA( A -94 ) ASP( A -93 ) ILE( A -92 ) THR( A -91 ) ALA( A -90 ) SER( A -89 ) LEU( A -88 ) LEU( A -87 ) GLN( A -86 ) GLN( A -85 ) ALA( A -84 ) ALA( A -83 ) GLY( A -82 ) LEU( A -81 ) ALA( A -80 ) GLU( A -79 ) VAL( A -78 ) VAL( A -77 ) ARG( A -76 ) ASP( A -75 ) PRO( A -74 ) LEU( A -73 ) ALA( A -72 ) PHE( A -71 ) LEU( A -70 ) ASP( A -69 ) GLU( A -68 ) PRO( A -67 ) GLU( A -66 ) ALA( A -65 ) GLY( A -64 ) ALA( A -63 ) GLY( A -62 ) ALA( A -61 ) ARG( A -60 ) PRO( A -59 ) ALA( A -58 ) ASN( A -57 ) ALA( A -56 ) PRO( A -55 ) GLU( A -54 ) VAL( A -53 ) LEU( A -52 ) LEU( A -51 ) VAL( A -50 ) GLY( A -49 ) THR( A -48 ) GLY( A -47 ) ARG( A -46 ) ARG( A -45 ) GLN( A -44 ) HIS( A -43 ) LEU( A -42 ) LEU( A -41 ) GLY( A -40 ) PRO( A -39 ) GLU( A -38 ) GLN( A -37 ) VAL( A -36 ) ARG( A -35 ) PRO( A -34 ) LEU( A -33 ) LEU( A -32 ) ALA( A -31 ) MSE( A -30 ) GLY( A -29 ) VAL( A -28 ) GLY( A -27 ) VAL( A -26 ) GLU( A -25 ) ALA( A -24 ) MSE( A -23 ) ASP( A -22 ) THR( A -21 ) GLN( A -20 ) ALA( A -19 ) ALA( A -18 ) ALA( A -17 ) ARG( A -16 ) THR( A -15 ) TYR( A -14 ) ASN( A -13 ) ILE( A -12 ) LEU( A -11 ) MSE( A -10 ) ALA( A -9 ) GLU( A -8 ) GLY( A -7 ) ARG( A -6 ) ARG( A -5 ) VAL( A -4 ) VAL( A -3 ) VAL( A -2 ) ALA( A -1 ) LEU( A 0 ) LEU( A 1 ) PRO( A 2 ) ASP( A 3 ) GLY( A 4 ) ASP( A 5 ) SER( A 6 ) SEQUENCE WARNING: Residue (A ALA 64 ) and Residue (A ALA 88 ) are not linked Distance of C-N bond is 5.19 PDB Chain_ID: A 1 15 SEQRES: MSE LYS LEU HIS THR ASP PRO ALA THR ALA LEU ASN THR VAL THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ALA TYR GLY ASP GLY TYR ILE GLU VAL ASN GLN VAL ARG PHE SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: HIS ALA ILE ALA PHE ALA PRO GLU GLY PRO VAL ALA SER TRP PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: VAL GLN ARG PRO ALA ASP ILE THR ALA SER LEU LEU GLN GLN ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ALA GLY LEU ALA GLU VAL VAL ARG ASP PRO LEU ALA PHE LEU ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: GLU PRO GLU ALA GLY ALA GLY ALA ARG PRO ALA ASN ALA PRO GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: VAL LEU LEU VAL GLY THR GLY ARG ARG GLN HIS LEU LEU GLY PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: GLU GLN VAL ARG PRO LEU LEU ALA MSE GLY VAL GLY VAL GLU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 121 135 SEQRES: MSE ASP THR GLN ALA ALA ALA ARG THR TYR ASN ILE LEU MSE ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 136 150 SEQRES: GLU GLY ARG ARG VAL VAL VAL ALA LEU LEU PRO ASP GLY ASP SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 151 165 SEQRES: PRO ALA THR ALA LEU ASN THR VAL THR ALA TYR GLY ASP GLY TYR COORDS: PRO ALA THR ALA LEU ASN THR VAL THR ALA TYR GLY ASP GLY TYR 7 21 166 180 SEQRES: ILE GLU VAL ASN GLN VAL ARG PHE SER HIS ALA ILE ALA PHE ALA COORDS: ILE GLU VAL ASN GLN VAL ARG PHE SER HIS ALA ILE ALA PHE ALA 22 36 181 195 SEQRES: PRO GLU GLY PRO VAL ALA SER TRP PRO VAL GLN ARG PRO ALA ASP COORDS: PRO GLU GLY PRO VAL ALA SER TRP PRO VAL GLN ARG PRO ALA ASP 37 51 196 210 SEQRES: ILE THR ALA SER LEU LEU GLN GLN ALA ALA GLY LEU ALA ALA PRO COORDS: ILE THR ALA SER LEU LEU GLN GLN ALA ALA GLY LEU ALA ALA PRO 52 89 211 225 SEQRES: GLU VAL LEU LEU VAL GLY THR GLY ARG ARG GLN HIS LEU LEU GLY COORDS: GLU VAL LEU LEU VAL GLY THR GLY ARG ARG GLN HIS LEU LEU GLY 90 104 226 240 SEQRES: PRO GLU GLN VAL ARG PRO LEU LEU ALA MET GLY VAL GLY VAL GLU COORDS: PRO GLU GLN VAL ARG PRO LEU LEU ALA MET GLY VAL GLY VAL GLU 105 119 241 255 SEQRES: ALA MET ASP THR GLN ALA ALA ALA ARG THR TYR ASN ILE LEU MET COORDS: ALA MET ASP THR GLN ALA ALA ALA ARG THR TYR ASN ILE LEU MET 120 134 256 268 SEQRES: ALA GLU GLY ARG ARG VAL VAL VAL ALA LEU LEU PRO ASP COORDS: ALA GLU GLY ARG ARG VAL VAL VAL ALA LEU LEU PRO ASP 135 147 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS ARG( A 48) CG CD NE CZ NH1 NH2 LEU( A 63) CG CD1 CD2 GLU( A 106) CG CD OE1 OE2 MET( A 114) SD MET( A 121) SD MET( A 134) SD ARG( A 139) CG CD NE CZ NH1 NH2 ASP( A 147) CG OD1 OD2 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS MET( A 114) SE MET( A 121) SE MET( A 134) SE BER31_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 114) in Token 'MODRES' can not be found in coordinates BER31_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 121) in Token 'MODRES' can not be found in coordinates BER31_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 134) in Token 'MODRES' can not be found in coordinates BER31_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 121) in Token 'SHEET' can not be found in coordinates