Read libraries from system resource. Wattos started at: April 20, 2007 11:49:16 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/pdb1kkw.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 12680 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 755 Found number of new bond candidates: 682 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: 34 Found number of new hydrogen bonds: 34 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 1(C ) 1 O6 9(G ) 2 1 1 2.994 122.685 5 N4 1(C ) 1 O6 10(G ) 2 1 1 2.885 132.466 5 N4 2(C ) 1 O6 9(G ) 2 1 1 3.037 151.492 5 N6 3(A ) 1 O4 8(T ) 2 1 1 2.935 148.530 5 N3 4(T ) 1 O6 7(G ) 2 1 1 2.813 134.034 5 N3 4(T ) 1 N1 7(G ) 2 1 1 3.191 140.745 5 N1 5(G ) 1 N3 6(C ) 2 1 1 2.946 155.347 5 N2 5(G ) 1 O2 6(C ) 2 1 1 2.957 163.493 5 N4 6(C ) 1 O6 5(G ) 2 1 1 2.878 145.603 5 N1 7(G ) 1 O2 4(T ) 2 1 1 3.072 160.748 5 N1 7(G ) 1 N3 4(T ) 2 1 1 3.200 137.351 5 N3 8(T ) 1 N1 3(A ) 2 1 1 2.889 167.204 5 N1 9(G ) 1 O2 2(C ) 2 1 1 3.099 141.875 5 N1 9(G ) 1 N3 2(C ) 2 1 1 2.960 150.347 5 N2 9(G ) 1 O2 2(C ) 2 1 1 2.878 154.063 5 N1 10(G ) 1 N3 1(C ) 2 1 1 2.904 159.254 5 N2 10(G ) 1 O2 1(C ) 2 1 1 2.992 169.189 5 N4 1(C ) 2 O6 9(G ) 1 1 1 2.995 121.942 5 N4 1(C ) 2 O6 10(G ) 1 1 1 2.886 132.755 5 N4 2(C ) 2 O6 9(G ) 1 1 1 3.038 151.784 5 N6 3(A ) 2 O4 8(T ) 1 1 1 2.949 146.430 5 N3 4(T ) 2 O6 7(G ) 1 1 1 2.824 133.678 5 N3 4(T ) 2 N1 7(G ) 1 1 1 3.200 140.465 5 N1 5(G ) 2 N3 6(C ) 1 1 1 2.945 158.300 5 N2 5(G ) 2 O2 6(C ) 1 1 1 2.945 166.219 5 N4 6(C ) 2 O6 5(G ) 1 1 1 2.873 141.437 5 N1 7(G ) 2 O2 4(T ) 1 1 1 3.062 162.007 5 N1 7(G ) 2 N3 4(T ) 1 1 1 3.191 136.266 5 N3 8(T ) 2 N1 3(A ) 1 1 1 2.897 168.122 5 N1 9(G ) 2 O2 2(C ) 1 1 1 3.103 142.017 5 N1 9(G ) 2 N3 2(C ) 1 1 1 2.960 150.552 5 N2 9(G ) 2 O2 2(C ) 1 1 1 2.881 154.311 5 N1 10(G ) 2 N3 1(C ) 1 1 1 2.901 159.614 5 N2 10(G ) 2 O2 1(C ) 1 1 1 2.991 169.308 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, 1kkw_wc.csv] Trying to match bases to eachother for number of bases: 20 Considering number of hydrogen bonds: 34 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 8( T) Mol: 2 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( T) Mol: 1 Model: 1 Entry: 1 Residue: 3( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1kkw_wc.csv Wattos started at: April 20, 2007 11:49:16 AM CDT Wattos stopped at: April 20, 2007 11:49:21 AM CDT Wattos took (#ms): 5133