Read libraries from system resource. Wattos started at: April 20, 2007 11:54:28 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/pdb1ttd.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 761 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 921 Found number of new bond candidates: 821 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: 40 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 12(G ) 1 O2 1(C ) 2 1 1 159.484 5 N2 12(G ) 1 N3 1(C ) 2 1 1 138.383 5 N2 12(G ) 1 O2 2(T ) 2 1 1 108.209 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 9(G ) 2 O2 4(C ) 1 1 1 155.753 5 N2 9(G ) 2 O4* 5(G ) 1 1 1 104.998 5 N2 9(G ) 2 O4* 10(T ) 2 1 1 118.482 5 Found number of new hydrogen bonds: 40 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 12(C ) 2 1 1 3.004 177.675 5 N2 1(G ) 1 O2 12(C ) 2 1 1 3.080 177.746 5 N4 2(C ) 1 O6 11(G ) 2 1 1 2.737 116.767 5 N6 3(A ) 1 O4 10(T ) 2 1 1 2.976 160.679 5 N4 4(C ) 1 O6 9(G ) 2 1 1 2.923 153.716 5 N1 5(G ) 1 O2 8(C ) 2 1 1 3.192 145.340 5 N1 5(G ) 1 N3 8(C ) 2 1 1 2.985 152.928 5 N2 5(G ) 1 O2 8(C ) 2 1 1 3.036 155.587 5 N6 6(A ) 1 N3 7(T ) 2 1 1 3.314 137.168 5 N6 6(A ) 1 O4 7(T ) 2 1 1 2.909 148.899 5 N6 7(A ) 1 O4 6(T ) 2 1 1 2.898 160.526 5 N3 8(T ) 1 N1 5(A ) 2 1 1 2.828 145.979 5 N3 9(T ) 1 N1 4(A ) 2 1 1 3.187 163.940 5 N6 10(A ) 1 O4 2(T ) 2 1 1 3.038 129.733 5 N6 10(A ) 1 O4 3(T ) 2 1 1 2.805 136.598 5 N6 11(A ) 1 N4 1(C ) 2 1 1 3.057 112.946 5 N6 11(A ) 1 O4 2(T ) 2 1 1 2.899 147.708 5 N1 12(G ) 1 N3 1(C ) 2 1 1 2.978 152.996 5 N2 12(G ) 1 O2 1(C ) 2 1 1 2.948 159.484 5 N2 12(G ) 1 N3 1(C ) 2 1 1 3.281 138.383 5 N2 12(G ) 1 O2 2(T ) 2 1 1 2.999 108.209 5 N4 1(C ) 2 N6 11(A ) 1 1 1 3.057 109.850 5 N4 1(C ) 2 O6 12(G ) 1 1 1 2.994 151.279 5 N3 2(T ) 2 N1 11(A ) 1 1 1 2.987 157.106 5 N3 3(T ) 2 N1 10(A ) 1 1 1 3.088 155.176 5 N6 4(A ) 2 O4 9(T ) 1 1 1 2.849 148.443 5 N6 5(A ) 2 O4 8(T ) 1 1 1 2.851 131.009 5 N3 6(T ) 2 N1 7(A ) 1 1 1 2.879 167.334 5 N3 7(T ) 2 N6 6(A ) 1 1 1 3.314 136.280 5 N3 7(T ) 2 N1 6(A ) 1 1 1 3.041 163.281 5 N4 8(C ) 2 O6 5(G ) 1 1 1 2.867 151.657 5 N1 9(G ) 2 O2 4(C ) 1 1 1 3.120 142.906 5 N1 9(G ) 2 N3 4(C ) 1 1 1 2.962 153.567 5 N2 9(G ) 2 O2 4(C ) 1 1 1 2.905 155.753 5 N2 9(G ) 2 O4* 5(G ) 1 1 1 3.014 104.998 5 N2 9(G ) 2 O4* 10(T ) 2 1 1 3.037 118.482 5 N3 10(T ) 2 N1 3(A ) 1 1 1 3.092 162.279 5 N1 11(G ) 2 N3 2(C ) 1 1 1 2.815 127.882 5 N2 11(G ) 2 O2 2(C ) 1 1 1 3.080 155.820 5 N4 12(C ) 2 O6 1(G ) 1 1 1 2.821 147.032 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, 1ttd_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 40 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 10( T) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 2 Model: 1 Entry: 1 Residue: 10( A) Mol: 1 Model: 1 Entry: 1 Residue: 3( T) Mol: 2 Model: 1 Entry: 1 Residue: 11( A) Mol: 1 Model: 1 Entry: 1 Residue: 2( T) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1ttd_wc.csv Wattos started at: April 20, 2007 11:54:28 AM CDT Wattos stopped at: April 20, 2007 11:54:31 AM CDT Wattos took (#ms): 2775