Read libraries from system resource. Wattos started at: January 19, 2007 10:15:46 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/pdb1bn0.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 7128 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 800 Found number of new bond candidates: 699 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: 22 Found number of new hydrogen bonds: 22 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 20(C ) 1 1 1 2.963 173.273 5 N2 1(G ) 1 O2 20(C ) 1 1 1 3.018 160.955 5 N1 2(G ) 1 N3 19(C ) 1 1 1 3.026 164.907 5 N2 2(G ) 1 O2 19(C ) 1 1 1 2.898 162.132 5 N6 3(A ) 1 O4 18(U ) 1 1 1 2.773 173.791 5 N4 4(C ) 1 O6 17(G ) 1 1 1 3.126 163.746 5 N3 5(U ) 1 N1 16(A ) 1 1 1 3.073 167.127 5 N6 6(A ) 1 O4 15(U ) 1 1 1 2.838 159.159 5 N1 7(G ) 1 N3 14(C ) 1 1 1 2.955 169.644 5 N2 7(G ) 1 O2 14(C ) 1 1 1 3.003 167.861 5 N4 8(C ) 1 O6 13(G ) 1 1 1 3.027 168.334 5 N1 13(G ) 1 N3 8(C ) 1 1 1 2.973 154.841 5 N2 13(G ) 1 O2 8(C ) 1 1 1 2.839 155.696 5 N4 14(C ) 1 O6 7(G ) 1 1 1 2.913 152.481 5 N3 15(U ) 1 N1 6(A ) 1 1 1 3.075 161.066 5 O2* 16(A ) 1 O4* 17(G ) 1 1 1 2.716 168.949 5 N6 16(A ) 1 O4 5(U ) 1 1 1 2.903 153.301 5 N1 17(G ) 1 N3 4(C ) 1 1 1 2.849 167.168 5 N2 17(G ) 1 O2 4(C ) 1 1 1 2.976 165.584 5 N3 18(U ) 1 N1 3(A ) 1 1 1 3.069 166.189 5 N4 19(C ) 1 O6 2(G ) 1 1 1 3.093 162.744 5 N4 20(C ) 1 O6 1(G ) 1 1 1 3.107 168.354 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, 1bn0_wc.csv] Trying to match bases to eachother for number of bases: 20 Considering number of hydrogen bonds: 22 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 19( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 18( U) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( U) Mol: 1 Model: 1 Entry: 1 Residue: 16( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 15( U) Mol: 1 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1bn0_wc.csv Wattos started at: January 19, 2007 10:15:46 AM CST Wattos stopped at: January 19, 2007 10:15:51 AM CST Wattos took (#ms): 4871