Read libraries from system resource. Wattos started at: April 20, 2007 11:46:00 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/pdb1bn9.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 946 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1124 Found number of new bond candidates: 1019 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: 38 Found number of new hydrogen bonds: 38 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 1(T ) 1 N1 15(A ) 2 1 1 2.969 177.997 5 N6 2(A ) 1 O4 14(T ) 2 1 1 3.034 173.079 5 N1 3(G ) 1 N3 13(C ) 2 1 1 2.998 171.649 5 N2 3(G ) 1 O2 13(C ) 2 1 1 2.941 171.360 5 N6 4(A ) 1 O4 12(T ) 2 1 1 3.048 168.808 5 N6 5(A ) 1 O4 11(T ) 2 1 1 2.990 163.869 5 N3 6(T ) 1 N1 10(A ) 2 1 1 2.970 179.357 5 N1 7(G ) 1 N3 9(C ) 2 1 1 2.994 170.213 5 N2 7(G ) 1 O2 9(C ) 2 1 1 2.909 179.374 5 N3 8(T ) 1 N1 8(A ) 2 1 1 2.967 178.221 5 N6 9(A ) 1 O4 7(T ) 2 1 1 2.964 171.254 5 N1 10(G ) 1 N3 6(C ) 2 1 1 2.992 169.773 5 N2 10(G ) 1 O2 6(C ) 2 1 1 2.926 175.254 5 N1 11(G ) 1 N3 5(C ) 2 1 1 2.994 167.747 5 N2 11(G ) 1 O2 5(C ) 2 1 1 2.894 174.217 5 N3 12(T ) 1 N1 4(A ) 2 1 1 2.985 178.822 5 N4 13(C ) 1 O6 3(G ) 2 1 1 2.963 165.008 5 N6 14(A ) 1 O4 2(T ) 2 1 1 2.939 168.655 5 N1 15(G ) 1 N3 1(C ) 2 1 1 2.999 174.684 5 N2 15(G ) 1 O2 1(C ) 2 1 1 2.943 174.085 5 N2 15(G ) 1 O2 2(T ) 2 1 1 3.026 101.400 5 N4 1(C ) 2 O6 15(G ) 1 1 1 2.930 161.146 5 N3 2(T ) 2 N1 14(A ) 1 1 1 2.996 173.219 5 N1 3(G ) 2 N3 13(C ) 1 1 1 2.982 172.391 5 N2 3(G ) 2 O2 13(C ) 1 1 1 2.911 170.404 5 N6 4(A ) 2 O4 12(T ) 1 1 1 2.955 177.191 5 N4 5(C ) 2 O6 11(G ) 1 1 1 2.983 164.868 5 N4 6(C ) 2 O6 10(G ) 1 1 1 2.950 170.081 5 N3 7(T ) 2 N1 9(A ) 1 1 1 2.968 176.973 5 N6 8(A ) 2 O4 8(T ) 1 1 1 2.994 164.502 5 N4 9(C ) 2 O6 7(G ) 1 1 1 2.971 164.687 5 N6 10(A ) 2 O4 6(T ) 1 1 1 2.968 166.386 5 N3 11(T ) 2 N1 5(A ) 1 1 1 2.963 176.053 5 N3 12(T ) 2 N1 4(A ) 1 1 1 2.920 172.400 5 N4 13(C ) 2 O6 3(G ) 1 1 1 2.935 166.547 5 N3 14(T ) 2 N1 2(A ) 1 1 1 2.925 177.461 5 N6 15(A ) 2 O4 1(T ) 1 1 1 2.971 163.605 5 N6 15(A ) 2 O4 14(T ) 2 1 1 3.100 106.359 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, 1bn9_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 38 Results contains number of sets of co-planar bases: 15 Results: Residue: 1( T) Mol: 1 Model: 1 Entry: 1 Residue: 15( A) Mol: 2 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 14( T) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 12( T) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 11( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( T) Mol: 1 Model: 1 Entry: 1 Residue: 10( A) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( T) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 12( T) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 2 Model: 1 Entry: 1 Residue: 14( A) Mol: 1 Model: 1 Entry: 1 Residue: 2( T) Mol: 2 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1bn9_wc.csv Wattos started at: April 20, 2007 11:46:00 AM CDT Wattos stopped at: April 20, 2007 11:46:03 AM CDT Wattos took (#ms): 3147