Read libraries from system resource. Wattos started at: April 20, 2007 11:46:20 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/pdb1coc.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: 916 Found number of new bond candidates: 819 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: 43 Found number of new hydrogen bonds: 43 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 2.929 165.308 5 N2 1(G ) 1 O4* 2(C ) 1 1 1 3.160 133.616 5 N2 1(G ) 1 O2 12(C ) 2 1 1 3.066 167.731 5 N4 2(C ) 1 O6 11(G ) 2 1 1 2.891 145.073 5 N6 3(A ) 1 O4 10(T ) 2 1 1 3.073 160.377 5 N4 4(C ) 1 O6 9(G ) 2 1 1 3.033 149.017 5 N1 5(G ) 1 O2 8(C ) 2 1 1 3.347 138.430 5 N1 5(G ) 1 N3 8(C ) 2 1 1 2.933 162.032 5 N2 5(G ) 1 O2 8(C ) 2 1 1 2.949 161.776 5 N6 6(A ) 1 O4 7(T ) 2 1 1 2.891 158.574 5 N6 7(A ) 1 O4 6(T ) 2 1 1 2.796 134.848 5 N6 7(A ) 1 O4 7(T ) 2 1 1 3.229 122.772 5 N3 8(T ) 1 N1 5(A ) 2 1 1 3.113 161.710 5 N3 9(T ) 1 N1 4(A ) 2 1 1 2.939 151.985 5 N3 9(T ) 1 N1 5(A ) 2 1 1 3.065 105.647 5 N6 10(A ) 1 O4 3(T ) 2 1 1 2.855 142.958 5 N6 11(A ) 1 N3 2(T ) 2 1 1 3.011 122.228 5 N6 11(A ) 1 O4 2(T ) 2 1 1 2.647 97.936 5 N1 12(G ) 1 O2 1(C ) 2 1 1 3.234 144.482 5 N1 12(G ) 1 N3 1(C ) 2 1 1 2.927 152.303 5 N2 12(G ) 1 O2 1(C ) 2 1 1 3.015 157.858 5 N4 1(C ) 2 N6 11(A ) 1 1 1 3.142 121.708 5 N4 1(C ) 2 O6 12(G ) 1 1 1 2.905 139.869 5 N3 2(T ) 2 N6 11(A ) 1 1 1 3.011 117.546 5 N3 2(T ) 2 N1 11(A ) 1 1 1 3.007 145.669 5 N3 3(T ) 2 N1 10(A ) 1 1 1 3.130 160.287 5 N6 4(A ) 2 O4 9(T ) 1 1 1 2.858 128.617 5 N6 5(A ) 2 O4 8(T ) 1 1 1 2.799 124.189 5 N6 5(A ) 2 O4 9(T ) 1 1 1 3.005 131.092 5 N3 6(T ) 2 N1 7(A ) 1 1 1 3.127 164.968 5 N3 7(T ) 2 N1 6(A ) 1 1 1 2.998 160.577 5 N3 7(T ) 2 N1 7(A ) 1 1 1 3.018 100.515 5 N4 8(C ) 2 O6 5(G ) 1 1 1 2.882 144.086 5 N4 8(C ) 2 N6 6(A ) 1 1 1 3.120 113.219 5 N1 9(G ) 2 O2 4(C ) 1 1 1 3.070 141.308 5 N1 9(G ) 2 N3 4(C ) 1 1 1 2.982 154.602 5 N2 9(G ) 2 O2 4(C ) 1 1 1 2.886 153.008 5 N2 9(G ) 2 O4* 10(T ) 2 1 1 3.023 105.612 5 N3 10(T ) 2 N1 3(A ) 1 1 1 2.911 165.021 5 N1 11(G ) 2 O2 2(C ) 1 1 1 3.060 148.562 5 N1 11(G ) 2 N3 2(C ) 1 1 1 2.947 146.590 5 N2 11(G ) 2 O2 2(C ) 1 1 1 3.029 151.677 5 N4 12(C ) 2 O6 1(G ) 1 1 1 2.940 138.390 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, 1coc_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 43 WARNING: Ignoring potential pair between consequetive bases: Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 WARNING: Ignoring potential pair between consequetive bases: Residue: 9( T) Mol: 1 Model: 1 Entry: 1 Residue: 8( T) Mol: 1 Model: 1 Entry: 1 Results contains number of sets of co-planar bases: 12 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: 8( T) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) 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: 1coc_wc.csv Wattos started at: April 20, 2007 11:46:20 AM CDT Wattos stopped at: April 20, 2007 11:46:23 AM CDT Wattos took (#ms): 2813