Read libraries from system resource. Wattos started at: April 20, 2007 11:47:40 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/pdb1ir5.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 21580 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1348 Found number of new bond candidates: 1162 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: 26 Found number of new hydrogen bonds: 26 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 3(C ) 1 O6 15(G ) 2 1 1 2.971 113.500 5 N3 4(T ) 1 N1 14(A ) 2 1 1 3.008 134.082 5 N3 7(T ) 1 N1 11(A ) 2 1 1 2.874 158.438 5 N4 8(C ) 1 N6 9(A ) 2 1 1 2.055 118.875 5 N4 8(C ) 1 O6 10(G ) 2 1 1 2.798 124.168 5 N3 9(T ) 1 N1 9(A ) 2 1 1 2.958 135.651 5 N3 10(T ) 1 N1 8(A ) 2 1 1 2.772 134.174 5 N3 11(T ) 1 N7 12(G ) 1 1 1 2.646 98.521 5 N3 11(T ) 1 N1 7(A ) 2 1 1 2.957 122.256 5 N1 12(G ) 1 N3 6(C ) 2 1 1 2.907 133.958 5 N3 13(T ) 1 N1 5(A ) 2 1 1 2.834 126.707 5 N1 15(G ) 1 N3 3(C ) 2 1 1 2.845 139.893 5 N3 16(T ) 1 N1 2(A ) 2 1 1 2.860 112.200 5 N1 17(G ) 1 N3 1(C ) 2 1 1 2.820 111.404 5 N3 4(T ) 2 N1 14(A ) 1 1 1 2.918 123.095 5 N6 5(A ) 2 O4 13(T ) 1 1 1 2.921 141.151 5 N4 6(C ) 2 O6 12(G ) 1 1 1 2.736 117.143 5 N6 9(A ) 2 O4 9(T ) 1 1 1 2.806 117.084 5 N1 10(G ) 2 O2 8(C ) 1 1 1 3.230 141.090 5 N1 10(G ) 2 N3 8(C ) 1 1 1 2.802 143.468 5 N1 12(G ) 2 N3 6(C ) 1 1 1 2.856 128.779 5 N3 13(T ) 2 N1 5(A ) 1 1 1 2.859 149.985 5 N1 15(G ) 2 N3 3(C ) 1 1 1 2.886 169.130 5 N3 16(T ) 2 N1 2(A ) 1 1 1 2.814 145.060 5 N1 17(G ) 2 N3 1(C ) 1 1 1 2.842 122.962 5 N1 17(G ) 2 N4 1(C ) 1 1 1 2.372 115.466 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, 1ir5_wc.csv] Trying to match bases to eachother for number of bases: 34 Considering number of hydrogen bonds: 26 Results contains number of sets of co-planar bases: 5 Results: Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 13( T) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1ir5_wc.csv Wattos started at: April 20, 2007 11:47:40 AM CDT Wattos stopped at: April 20, 2007 11:47:47 AM CDT Wattos took (#ms): 6913