May. 10, 07:01:12 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 0.8 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-115 ) GLY( A-114 ) HIS( A-113 ) HIS( A-112 ) HIS( A-111 ) HIS( A-110 ) HIS( A-109 ) HIS( A-108 ) SER( A-107 ) HIS( A-106 ) VAL( A-105 ) ALA( A-104 ) GLN( A-103 ) PHE( A-102 ) PRO( A-101 ) THR( A-100 ) PRO( A -99 ) PHE( A -98 ) GLY( A -97 ) GLY( A -96 ) SER( A -95 ) LEU( A -94 ) ASP( A -93 ) THR( A -92 ) TRP( A -91 ) ALA( A -90 ) ILE( A -89 ) THR( A -88 ) VAL( A -87 ) GLU( A -86 ) GLU( A -85 ) ARG( A -84 ) ALA( A -83 ) LYS( A -82 ) HIS( A -81 ) ASP( A -80 ) GLN( A -79 ) GLN( A -78 ) PHE( A -77 ) HIS( A -76 ) SER( A -75 ) LEU( A -74 ) LYS( A -73 ) PRO( A -72 ) ILE( A -71 ) SER( A -70 ) GLY( A -69 ) PHE( A -68 ) ILE( A -67 ) THR( A -66 ) GLY( A -65 ) ASP( A -64 ) GLN( A -63 ) ALA( A -62 ) ARG( A -61 ) ASN( A -60 ) PHE( A -59 ) PHE( A -58 ) PHE( A -57 ) GLN( A -56 ) SER( A -55 ) GLY( A -54 ) LEU( A -53 ) PRO( A -52 ) GLN( A -51 ) PRO( A -50 ) VAL( A -49 ) LEU( A -48 ) ALA( A -47 ) GLN( A -46 ) ILE( A -45 ) TRP( A -44 ) ALA( A -43 ) LEU( A -42 ) ALA( A -41 ) ASP( A -40 ) MSE( A -39 ) ASN( A -38 ) ASN( A -37 ) ASP( A -36 ) GLY( A -35 ) ARG( A -34 ) MSE( A -33 ) ASP( A -32 ) GLN( A -31 ) VAL( A -30 ) GLU( A -29 ) PHE( A -28 ) SER( A -27 ) ILE( A -26 ) ALA( A -25 ) MSE( A -24 ) LYS( A -23 ) LEU( A -22 ) ILE( A -21 ) LYS( A -20 ) LEU( A -19 ) LYS( A -18 ) LEU( A -17 ) GLN( A -16 ) GLY( A -15 ) TYR( A -14 ) GLN( A -13 ) LEU( A -12 ) PRO( A -11 ) SER( A -10 ) ALA( A -9 ) LEU( A -8 ) PRO( A -7 ) PRO( A -6 ) VAL( A -5 ) MSE( A -4 ) LYS( A -3 ) GLN( A -2 ) GLN( A -1 ) PRO( A 0 ) VAL( A 1 ) ALA( A 2 ) ILE( A 3 ) SER( A 4 ) SER( A 5 ) PDB Chain_ID: A 1 15 SEQRES: MSE GLY HIS HIS HIS HIS HIS HIS SER HIS VAL ALA GLN PHE PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE GLN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU PRO COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: SER ALA LEU PRO PRO VAL MSE LYS GLN GLN PRO VAL ALA ILE SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 121 135 SEQRES: SER THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL COORDS: ... THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL 6 19 136 150 SEQRES: GLU GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO COORDS: GLU GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO 20 34 151 165 SEQRES: ILE SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE COORDS: ILE SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE 35 49 166 180 SEQRES: GLN SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU COORDS: GLN SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU 50 64 181 195 SEQRES: ALA ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER COORDS: ALA ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER 65 79 196 210 SEQRES: ILE ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU COORDS: ILE ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU 80 94 211 219 SEQRES: PRO SER ALA LEU PRO PRO VAL MSE LYS COORDS: PRO SER ALA LEU PRO PRO VAL MSE LYS 95 103 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS THR( A 6) OG1 CG2 HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 403) in Token 'SITE' can not be found in coordinates HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 465) in Token 'SITE' can not be found in coordinates HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 485) in Token 'SITE' can not be found in coordinates HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 503) in Token 'SITE' can not be found in coordinates