Read libraries from system resource. Wattos started at: January 19, 2007 10:18:49 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/pdb1ow9.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 8250 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 952 Found number of new bond candidates: 811 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: 27 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 10(C ) 1 N6 9(A ) 1 1 1 102.758 5 N4 10(C ) 1 O6 11(G ) 1 1 1 123.764 5 N4 10(C ) 1 O6 15(G ) 1 1 1 141.238 5 Found number of new hydrogen bonds: 27 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N1 1(G ) 1 N3 23(C ) 1 1 1 2.933 150.843 5 N2 1(G ) 1 O2 23(C ) 1 1 1 2.967 134.819 5 N6 2(A ) 1 O4 22(U ) 1 1 1 2.911 143.400 5 N1 3(G ) 1 N3 21(C ) 1 1 1 2.984 158.686 5 N2 3(G ) 1 O2 21(C ) 1 1 1 2.973 153.596 5 N4 4(C ) 1 O6 20(G ) 1 1 1 2.823 157.713 5 N2 5(G ) 1 N6 6(A ) 1 1 1 2.491 105.325 5 N2 5(G ) 1 N7 19(A ) 1 1 1 3.162 156.746 5 N6 6(A ) 1 N9 18(G ) 1 1 1 3.159 116.087 5 N1 8(G ) 1 N3 17(C ) 1 1 1 2.928 164.868 5 N2 8(G ) 1 O2 17(C ) 1 1 1 2.995 149.362 5 N6 9(A ) 1 O4 16(U ) 1 1 1 2.846 135.045 5 N4 10(C ) 1 N6 9(A ) 1 1 1 2.740 102.758 5 N4 10(C ) 1 O6 11(G ) 1 1 1 2.784 123.764 5 N4 10(C ) 1 O6 15(G ) 1 1 1 3.033 141.238 5 N2 11(G ) 1 N7 14(A ) 1 1 1 2.845 137.968 5 N6 14(A ) 1 N3 11(G ) 1 1 1 2.990 141.768 5 N1 15(G ) 1 N3 10(C ) 1 1 1 3.044 159.023 5 N2 15(G ) 1 O2 10(C ) 1 1 1 2.947 162.353 5 N3 16(U ) 1 N1 9(A ) 1 1 1 2.942 166.921 5 N4 17(C ) 1 O6 8(G ) 1 1 1 2.990 156.301 5 N6 19(A ) 1 O2* 5(G ) 1 1 1 2.599 154.414 5 N1 20(G ) 1 N3 4(C ) 1 1 1 2.944 165.027 5 N2 20(G ) 1 O2 4(C ) 1 1 1 2.962 172.030 5 N4 21(C ) 1 O6 3(G ) 1 1 1 2.890 177.332 5 N3 22(U ) 1 N1 2(A ) 1 1 1 2.873 169.341 5 N4 23(C ) 1 O6 1(G ) 1 1 1 2.977 155.658 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, 1ow9_wc.csv] Trying to match bases to eachother for number of bases: 23 Considering number of hydrogen bonds: 27 Results contains number of sets of co-planar bases: 7 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 22( U) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 1 Model: 1 Entry: 1 Residue: 16( U) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1ow9_wc.csv Wattos started at: January 19, 2007 10:18:49 AM CST Wattos stopped at: January 19, 2007 10:18:53 AM CST Wattos took (#ms): 4449