Read libraries from system resource. Wattos started at: April 20, 2007 11:46:13 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/pdb1c32.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 4880 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 598 Found number of new bond candidates: 526 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: 32 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 5(G ) 1 N2 1(G ) 1 1 1 107.765 5 N2 5(G ) 1 N7 2(G ) 1 1 1 139.660 5 N2 5(G ) 1 O2P 4(T ) 1 1 1 94.136 5 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 11(G ) 1 N7 5(G ) 1 1 1 112.337 5 N2 11(G ) 1 O6 5(G ) 1 1 1 148.827 5 N2 11(G ) 1 O2 7(T ) 1 1 1 176.434 5 Found number of new hydrogen bonds: 32 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 6(G ) 1 1 1 2.583 169.928 5 N2 1(G ) 1 N2 5(G ) 1 1 1 2.992 100.706 5 N2 1(G ) 1 N7 6(G ) 1 1 1 2.806 163.609 5 N1 2(G ) 1 O6 14(G ) 1 1 1 2.582 157.649 5 N2 2(G ) 1 N7 14(G ) 1 1 1 3.099 149.634 5 N2 2(G ) 1 O6 14(G ) 1 1 1 3.001 127.303 5 N3 3(T ) 1 O1P 2(G ) 1 1 1 2.303 127.592 5 N3 4(T ) 1 O4 13(T ) 1 1 1 2.690 167.951 5 N1 5(G ) 1 N7 2(G ) 1 1 1 2.687 142.762 5 N1 5(G ) 1 O6 2(G ) 1 1 1 3.066 125.398 5 N2 5(G ) 1 N2 1(G ) 1 1 1 2.992 107.765 5 N2 5(G ) 1 N7 2(G ) 1 1 1 2.758 139.660 5 N2 5(G ) 1 O2P 4(T ) 1 1 1 2.860 94.136 5 N1 6(G ) 1 O6 10(G ) 1 1 1 2.553 170.023 5 N2 6(G ) 1 O3* 7(T ) 1 1 1 2.837 128.749 5 N2 6(G ) 1 N7 10(G ) 1 1 1 2.846 152.068 5 N1 8(G ) 1 O5* 1(G ) 1 1 1 2.574 172.848 5 N3 9(T ) 1 O1P 8(G ) 1 1 1 2.603 171.735 5 N1 10(G ) 1 O6 15(G ) 1 1 1 2.562 163.951 5 N2 10(G ) 1 N7 15(G ) 1 1 1 2.860 162.328 5 N2 10(G ) 1 O6 15(G ) 1 1 1 3.234 114.575 5 N1 11(G ) 1 O6 2(G ) 1 1 1 3.234 147.764 5 N1 11(G ) 1 O6 5(G ) 1 1 1 2.790 139.111 5 N2 11(G ) 1 N7 5(G ) 1 1 1 2.783 112.337 5 N2 11(G ) 1 O6 5(G ) 1 1 1 2.694 148.827 5 N2 11(G ) 1 O2 7(T ) 1 1 1 2.516 176.434 5 N3 12(T ) 1 O1P 11(G ) 1 1 1 2.350 167.842 5 N3 13(T ) 1 O4 4(T ) 1 1 1 2.766 160.080 5 N1 14(G ) 1 O6 11(G ) 1 1 1 2.727 135.450 5 N2 14(G ) 1 N7 11(G ) 1 1 1 2.831 165.135 5 N1 15(G ) 1 O6 1(G ) 1 1 1 2.675 178.217 5 N2 15(G ) 1 N7 1(G ) 1 1 1 2.861 156.760 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, 1c32_wc.csv] Trying to match bases to eachother for number of bases: 15 Considering number of hydrogen bonds: 32 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: 1c32_wc.csv Wattos started at: April 20, 2007 11:46:13 AM CDT Wattos stopped at: April 20, 2007 11:46:15 AM CDT Wattos took (#ms): 1163