Read libraries from system resource. Wattos started at: April 20, 2007 11:49:28 AM CDT Program arguments [1] :[-at] SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Read libraries from system resource. SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Enter property name: Enter property value (watch value type) for interactiveSession: Enter property name: Enter property value (watch value type) for verbosity: Enter property name: Enter property value (watch value type) for writeSessionOnExit: Enter property name: Enter property value (watch value type) for stopOnError: Enter url to (gzipped) PDB formatted coordinate file: Doing ReadEntryPDB with arguments: [file:/dumpzone/pdb/nozip/data/structures/all/pdb/pdb1kxl.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 30990 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 3642 Found number of new bond candidates: 3134 Hydrogen bond distance between proton and acceptor cutoff (2.7 Angstroms suggested) Hydrogen bond distance between donor and acceptor cutoff (3.35 Angstroms suggested) Hydrogen bond angle (D-H-A) cutoff (90 degrees suggested) Doing CalcHydrogenBond with arguments: [2.7, 3.35, 90.0] Found number of new hydrogen bond candidates: 87 Found number of new hydrogen bonds: 87 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 13(GLN) 1 N 12(CYS) 1 1 1 2.702 105.817 5 N 16(LEU) 1 N 15(GLY) 1 1 1 2.623 107.737 5 N 20(GLU) 1 N 19(PHE) 1 1 1 2.599 109.288 5 N 24(ILE) 1 O 122(ILE) 1 1 1 3.054 159.720 5 N 26(MET) 1 O 120(MET) 1 1 1 2.976 150.891 5 N 30(LEU) 1 N 29(MET) 1 1 1 2.633 108.923 5 N 31(VAL) 1 O 44(VAL) 1 1 1 3.021 139.277 5 N 32(SER) 1 N 31(VAL) 1 1 1 2.732 102.015 5 N 34(SER) 1 O 42(SER) 1 1 1 2.748 128.210 5 N 36(ASP) 1 N 35(PHE) 1 1 1 2.736 101.702 5 N 40(PHE) 1 N 39(ALA) 1 1 1 2.666 107.659 5 N 45(PHE) 1 O 76(PHE) 1 1 1 3.134 121.293 5 N 53(ILE) 1 N 52(ASP) 1 1 1 2.595 106.487 5 N 67(GLU) 1 N 66(TYR) 1 1 1 2.646 105.930 5 N 73(ASN) 1 N 72(LEU) 1 1 1 2.634 105.343 5 N 74(GLU) 1 N 73(ASN) 1 1 1 2.860 94.855 5 N 76(PHE) 1 O 45(PHE) 1 1 1 3.015 129.658 5 N 78(ALA) 1 O 43(PHE) 1 1 1 2.969 133.981 5 N 84(GLN) 1 N 83(ASN) 1 1 1 2.802 97.309 5 N 85(PHE) 1 O 82(LYS) 1 1 1 2.537 120.692 5 N 85(PHE) 1 N 84(GLN) 1 1 1 2.633 104.665 5 N 86(GLU) 1 O 82(LYS) 1 1 1 2.606 155.350 5 N 86(GLU) 1 N 85(PHE) 1 1 1 2.794 97.987 5 N 87(THR) 1 N 86(GLU) 1 1 1 2.823 94.998 5 N 88(PHE) 1 N 87(THR) 1 1 1 2.887 93.409 5 N 89(ASP) 1 O 85(PHE) 1 1 1 2.747 162.352 5 N 89(ASP) 1 N 88(PHE) 1 1 1 2.788 98.199 5 N 90(SER) 1 O 86(GLU) 1 1 1 2.460 160.043 5 N 92(LEU) 1 O 89(ASP) 1 1 1 2.590 115.799 5 N 92(LEU) 1 N 91(LYS) 1 1 1 2.675 101.970 5 N 93(ARG) 1 O 89(ASP) 1 1 1 2.531 162.312 5 N 93(ARG) 1 N 92(LEU) 1 1 1 2.822 97.915 5 N 94(LYS) 1 N 93(ARG) 1 1 1 2.712 102.534 5 N 95(ILE) 1 O 92(LEU) 1 1 1 2.606 140.318 5 N 95(ILE) 1 N 94(LYS) 1 1 1 2.695 103.926 5 N 96(PHE) 1 O 92(LEU) 1 1 1 3.151 137.294 5 N 96(PHE) 1 N 95(ILE) 1 1 1 2.614 105.146 5 N 97(ASN) 1 N 98(ASN) 1 1 1 2.706 99.303 5 N 98(ASN) 1 N 97(ASN) 1 1 1 2.706 104.685 5 N 101(ARG) 1 N 100(LEU) 1 1 1 2.726 102.176 5 N 102(ASP) 1 O 99(GLY) 1 1 1 2.427 143.035 5 N 102(ASP) 1 N 101(ARG) 1 1 1 2.690 104.571 5 N 103(LEU) 1 N 102(ASP) 1 1 1 2.700 102.181 5 N 106(GLY) 1 N 105(ASN) 1 1 1 2.723 102.554 5 N 122(ILE) 1 O 24(ILE) 1 1 1 3.048 161.529 5 N 123(LYS) 1 O 134(ILE) 1 1 1 2.798 150.488 5 N 124(VAL) 1 O 22(LYS) 1 1 1 3.231 131.196 5 N 129(GLY) 1 N 128(ASN) 1 1 1 2.640 107.024 5 N 130(LYS) 1 N 129(GLY) 1 1 1 2.666 106.174 5 N 132(ASN) 1 O 125(LYS) 1 1 1 2.609 149.631 5 N 136(ARG) 1 O 121(ASN) 1 1 1 2.619 169.849 5 N 137(GLU) 1 N 136(ARG) 1 1 1 2.730 101.602 5 N 139(GLU) 1 O 119(LYS) 1 1 1 2.990 148.989 5 N 141(VAL) 1 O 117(VAL) 1 1 1 2.794 142.212 5 N 147(SER) 1 N 146(ILE) 1 1 1 2.730 99.152 5 N 148(SER) 1 N 147(SER) 1 1 1 2.645 106.571 5 N 149(ILE) 1 N 148(SER) 1 1 1 2.596 107.813 5 N 150(ALA) 1 O 146(ILE) 1 1 1 2.614 159.384 5 N 150(ALA) 1 N 149(ILE) 1 1 1 2.771 97.618 5 N 155(CYS) 1 N 154(GLN) 1 1 1 2.688 104.110 5 N 156(GLU) 1 N 155(CYS) 1 1 1 2.770 99.760 5 N 158(LEU) 1 N 157(HIS) 1 1 1 2.762 99.054 5 N 159(ARG) 1 O 155(CYS) 1 1 1 3.143 153.866 5 N 159(ARG) 1 N 158(LEU) 1 1 1 2.773 97.688 5 N 160(LEU) 1 N 159(ARG) 1 1 1 2.889 92.716 5 N 161(PHE) 1 N 160(LEU) 1 1 1 2.706 102.160 5 N 162(TYR) 1 N 161(PHE) 1 1 1 2.705 101.349 5 N 163(GLN) 1 N 162(TYR) 1 1 1 2.702 101.777 5 N 164(ARG) 1 N 163(GLN) 1 1 1 2.728 101.088 5 N 165(ALA) 1 O 161(PHE) 1 1 1 2.900 150.094 5 N 166(PHE) 1 O 162(TYR) 1 1 1 3.041 145.266 5 N 166(PHE) 1 N 165(ALA) 1 1 1 2.757 100.231 5 N 167(LYS) 1 N 166(PHE) 1 1 1 2.801 97.888 5 N 168(ARG) 1 N 167(LYS) 1 1 1 2.857 95.492 5 N 169(ILE) 1 O 165(ALA) 1 1 1 2.559 152.903 5 N 169(ILE) 1 N 168(ARG) 1 1 1 2.860 95.740 5 N 172(SER) 1 N 171(GLU) 1 1 1 2.727 101.185 5 N 173(ALA) 1 N 172(SER) 1 1 1 2.828 95.484 5 N 175(SER) 1 N 174(ILE) 1 1 1 2.698 103.384 5 N 176(ARG) 1 O 173(ALA) 1 1 1 2.697 134.248 5 N 176(ARG) 1 N 175(SER) 1 1 1 2.703 103.183 5 N 177(TYR) 1 N 176(ARG) 1 1 1 2.772 99.747 5 N 178(PHE) 1 N 177(TYR) 1 1 1 2.841 94.599 5 N 179(GLU) 1 N 178(PHE) 1 1 1 2.854 96.532 5 N 181(TYR) 1 N 180(GLU) 1 1 1 2.869 96.647 5 N 182(ARG) 1 N 181(TYR) 1 1 1 2.799 101.075 5 N 183(ARG) 1 N 182(ARG) 1 1 1 2.675 107.671 5 Angle cutoff (40.0 degrees suggested) Use only Watson Crick basepairing (false suggested) (y/n): Enter cvs file name (with path) for output of CalcCoPlanarBasesSet.: Doing CalcCoPlanarBasesSet with arguments: [45.0, true, 1kxl_wc.csv] Trying to match bases to eachother for number of bases: 0 Considering number of hydrogen bonds: 87 WARNING: requested less than 1 new rows in getNewRowIdList: 0 Results contains number of sets of co-planar bases: 0 Results: Writing results to file: 1kxl_wc.csv Wattos started at: April 20, 2007 11:49:28 AM CDT Wattos stopped at: April 20, 2007 11:49:32 AM CDT Wattos took (#ms): 3890