Read libraries from system resource. Wattos started at: January 19, 2007 10:19:19 AM CST 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/pdb1rgo.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 28040 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1619 Found number of new bond candidates: 1446 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: 67 WARNING: Got more than two hydrogen bond for this donor (N). Hydrogen bonds (3) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 13(GLU) 1 O 9(CYS) 1 1 1 161.887 5 N 13(GLU) 1 O 10(ARG) 1 1 1 106.790 5 N 13(GLU) 1 N 12(PHE) 1 1 1 94.578 5 Found number of new hydrogen bonds: 67 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 4(TYR) 1 N 3(ARG) 1 1 1 2.739 103.270 5 N 5(LYS) 1 O 25(GLN) 1 1 1 2.767 168.231 5 N 6(THR) 1 N 5(LYS) 1 1 1 2.830 100.192 5 N 6(THR) 1 O4 6(U ) 3 1 1 3.084 121.248 5 N 7(GLU) 1 N 6(THR) 1 1 1 2.722 103.438 5 N 7(GLU) 1 O4 6(U ) 3 1 1 2.849 144.237 5 N 9(CYS) 1 O 27(ALA) 1 1 1 2.832 161.920 5 N 12(PHE) 1 N 11(PRO) 1 1 1 2.842 95.250 5 N 13(GLU) 1 O 9(CYS) 1 1 1 3.007 161.887 5 N 13(GLU) 1 O 10(ARG) 1 1 1 3.126 106.790 5 N 13(GLU) 1 N 12(PHE) 1 1 1 2.864 94.578 5 N 14(GLU) 1 O 10(ARG) 1 1 1 2.841 148.091 5 N 14(GLU) 1 N 13(GLU) 1 1 1 2.808 98.332 5 N 15(SER) 1 O 11(PRO) 1 1 1 2.971 169.727 5 N 15(SER) 1 N 14(GLU) 1 1 1 2.899 94.801 5 N 16(GLY) 1 O 12(PHE) 1 1 1 2.773 136.645 5 N 16(GLY) 1 N 15(SER) 1 1 1 2.750 103.828 5 N 20(TYR) 1 N 19(LYS) 1 1 1 2.742 102.940 5 N 21(GLY) 1 O 18(CYS) 1 1 1 3.158 148.681 5 N 21(GLY) 1 N 20(TYR) 1 1 1 2.754 101.856 5 N 23(LYS) 1 O 20(TYR) 1 1 1 3.070 151.318 5 N 23(LYS) 1 N 22(GLU) 1 1 1 2.741 103.688 5 N 24(CYS) 1 O 21(GLY) 1 1 1 3.164 167.376 5 N 24(CYS) 1 N 23(LYS) 1 1 1 2.722 103.994 5 N 25(GLN) 1 O2 8(U ) 3 1 1 2.820 169.106 5 N 26(PHE) 1 N 25(GLN) 1 1 1 2.735 102.635 5 N 27(ALA) 1 O 7(GLU) 1 1 1 2.957 176.095 5 N 29(GLY) 1 N 28(HIS) 1 1 1 2.774 98.830 5 N 31(HIS) 1 N 30(PHE) 1 1 1 2.751 101.580 5 N 32(GLU) 1 O 29(GLY) 1 1 1 2.925 164.373 5 N 32(GLU) 1 N 31(HIS) 1 1 1 2.766 102.830 5 N 33(LEU) 1 N 32(GLU) 1 1 1 2.736 102.600 5 N 41(LYS) 1 ND1 39(HIS) 1 1 1 3.022 164.496 5 N 41(LYS) 1 N 40(PRO) 1 1 1 2.796 100.133 5 N 42(TYR) 1 O 39(HIS) 1 1 1 2.926 146.650 5 N 42(TYR) 1 N 41(LYS) 1 1 1 2.767 102.023 5 N 43(LYS) 1 O 63(HIS) 1 1 1 2.776 165.900 5 N 44(THR) 1 O4 2(U ) 3 1 1 2.886 154.493 5 OG1 44(THR) 1 O 41(LYS) 1 1 1 2.806 172.478 5 N 45(GLU) 1 N 44(THR) 1 1 1 2.742 101.193 5 N 45(GLU) 1 O4 2(U ) 3 1 1 2.925 165.673 5 N 47(CYS) 1 O 65(ILE) 1 1 1 2.897 172.739 5 N 48(ARG) 1 N1 3(A ) 3 1 1 3.100 166.833 5 N 51(HIS) 1 O 47(CYS) 1 1 1 2.942 169.097 5 N 51(HIS) 1 N 50(PHE) 1 1 1 2.862 94.558 5 NE2 51(HIS) 1 O 66(HIS) 1 1 1 2.868 145.556 5 N 52(THR) 1 N 51(HIS) 1 1 1 2.760 103.675 5 OG1 52(THR) 1 O 48(ARG) 1 1 1 2.744 155.552 5 N 53(ILE) 1 O 49(THR) 1 1 1 2.787 143.675 5 N 54(GLY) 1 O 50(PHE) 1 1 1 3.101 125.751 5 N 54(GLY) 1 N 53(ILE) 1 1 1 2.742 102.800 5 N 55(PHE) 1 N 54(GLY) 1 1 1 2.710 103.764 5 N 58(TYR) 1 N 57(PRO) 1 1 1 2.742 102.211 5 N 59(GLY) 1 O 56(CYS) 1 1 1 3.093 148.973 5 N 59(GLY) 1 N 58(TYR) 1 1 1 2.740 101.637 5 N 61(ARG) 1 O 58(TYR) 1 1 1 3.200 139.416 5 N 61(ARG) 1 N 60(PRO) 1 1 1 2.745 102.534 5 N 62(CYS) 1 O 59(GLY) 1 1 1 3.136 163.817 5 N 62(CYS) 1 N 61(ARG) 1 1 1 2.731 103.618 5 N 63(HIS) 1 O2 4(U ) 3 1 1 2.851 174.485 5 N 64(PHE) 1 N 63(HIS) 1 1 1 2.738 102.278 5 N 65(ILE) 1 O 45(GLU) 1 1 1 2.883 161.565 5 N3 2(U ) 3 O 63(HIS) 1 1 1 2.819 169.735 5 N6 3(A ) 3 O 46(LEU) 1 1 1 2.888 171.044 5 N3 4(U ) 3 SG 62(CYS) 1 1 1 3.272 162.628 5 N3 6(U ) 3 O 25(GLN) 1 1 1 2.811 173.854 5 N6 7(A ) 3 O 8(LEU) 1 1 1 2.819 168.976 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, 1rgo_wc.csv] Trying to match bases to eachother for number of bases: 9 Considering number of hydrogen bonds: 67 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: 1rgo_wc.csv Wattos started at: January 19, 2007 10:19:19 AM CST Wattos stopped at: January 19, 2007 10:19:22 AM CST Wattos took (#ms): 2913