Read libraries from system resource. Wattos started at: April 20, 2007 11:54:33 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/pdb1u64.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 5728 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 878 Found number of new bond candidates: 772 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: 31 Found number of new hydrogen bonds: 31 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 O6 10(G ) 2 1 1 2.850 152.496 5 N2 1(G ) 1 N7 10(G ) 2 1 1 2.847 160.885 5 N1 2(G ) 1 O6 1(G ) 2 1 1 2.956 158.034 5 N2 2(G ) 1 N7 3(G ) 1 1 1 2.937 139.507 5 N2 2(G ) 1 N7 1(G ) 2 1 1 2.868 165.356 5 N1 8(G ) 1 O6 9(G ) 2 1 1 2.652 149.628 5 N2 8(G ) 1 N7 9(G ) 2 1 1 3.125 175.498 5 N1 9(G ) 1 O6 2(G ) 2 1 1 2.886 163.211 5 N2 9(G ) 1 N7 2(G ) 2 1 1 2.884 164.636 5 N1 10(G ) 1 O6 3(G ) 2 1 1 2.888 155.368 5 N2 10(G ) 1 N7 3(G ) 2 1 1 3.131 174.974 5 N2 11(G ) 1 O4 6(T ) 2 1 1 3.244 142.085 5 N2 11(G ) 1 O4 7(T ) 2 1 1 2.891 154.803 5 N1 1(G ) 2 O6 8(G ) 1 1 1 2.869 160.179 5 N2 1(G ) 2 N7 8(G ) 1 1 1 2.854 163.836 5 N1 2(G ) 2 O6 1(G ) 1 1 1 2.922 149.014 5 N2 2(G ) 2 N7 1(G ) 1 1 1 2.817 158.527 5 N1 3(G ) 2 O6 8(G ) 2 1 1 3.027 156.944 5 N2 3(G ) 2 N7 8(G ) 2 1 1 2.911 153.048 5 N3 6(T ) 2 O2 4(T ) 2 1 1 2.662 136.205 5 N3 7(T ) 2 O2 6(T ) 2 1 1 2.608 145.464 5 N1 8(G ) 2 N7 11(G ) 2 1 1 3.039 137.387 5 N1 8(G ) 2 O6 11(G ) 2 1 1 2.915 135.117 5 N2 8(G ) 2 N7 11(G ) 2 1 1 2.802 152.775 5 N1 9(G ) 2 O6 2(G ) 1 1 1 2.851 153.071 5 N2 9(G ) 2 N7 2(G ) 1 1 1 2.743 104.125 5 N2 9(G ) 2 O6 2(G ) 1 1 1 2.757 165.768 5 N1 10(G ) 2 O6 9(G ) 1 1 1 2.883 152.367 5 N2 10(G ) 2 N7 9(G ) 1 1 1 2.903 169.137 5 N1 11(G ) 2 O6 10(G ) 1 1 1 2.862 150.118 5 N2 11(G ) 2 N7 10(G ) 1 1 1 2.996 178.076 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, 1u64_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 31 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: 1u64_wc.csv Wattos started at: April 20, 2007 11:54:33 AM CDT Wattos stopped at: April 20, 2007 11:54:34 AM CDT Wattos took (#ms): 1582