Read libraries from system resource. Wattos started at: April 20, 2007 11:49:08 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/pdb1kkv.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 12600 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 755 Found number of new bond candidates: 678 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 3.164 116.196 5 N4 1(C ) 1 O6 10(G ) 2 1 1 2.940 152.858 5 N4 2(C ) 1 O6 9(G ) 2 1 1 2.915 151.318 5 N6 3(A ) 1 O6 7(G ) 2 1 1 2.833 95.449 5 N6 3(A ) 1 O4 8(T ) 2 1 1 3.065 157.694 5 N4 4(C ) 1 O6 7(G ) 2 1 1 2.873 150.283 5 N1 5(G ) 1 N3 6(C ) 2 1 1 2.954 168.747 5 N2 5(G ) 1 O2 6(C ) 2 1 1 2.965 178.087 5 N4 6(C ) 1 O6 5(G ) 2 1 1 2.888 153.000 5 N1 7(G ) 1 N3 4(C ) 2 1 1 2.919 156.322 5 N2 7(G ) 1 O2 4(C ) 2 1 1 2.947 165.316 5 N3 8(T ) 1 N1 3(A ) 2 1 1 2.774 139.132 5 N1 9(G ) 1 O2 2(C ) 2 1 1 3.326 138.027 5 N1 9(G ) 1 N3 2(C ) 2 1 1 2.905 158.083 5 N2 9(G ) 1 O2 2(C ) 2 1 1 2.890 163.060 5 N1 10(G ) 1 N3 1(C ) 2 1 1 2.957 164.088 5 N2 10(G ) 1 O2 1(C ) 2 1 1 2.930 171.641 5 N4 1(C ) 2 O6 9(G ) 1 1 1 3.067 116.109 5 N4 1(C ) 2 O6 10(G ) 1 1 1 2.939 150.134 5 N4 2(C ) 2 O6 9(G ) 1 1 1 2.905 150.113 5 N6 3(A ) 2 O6 7(G ) 1 1 1 2.816 92.212 5 N6 3(A ) 2 O4 8(T ) 1 1 1 3.042 156.669 5 N4 4(C ) 2 O6 7(G ) 1 1 1 2.892 151.055 5 N1 5(G ) 2 N3 6(C ) 1 1 1 2.934 163.055 5 N2 5(G ) 2 O2 6(C ) 1 1 1 2.937 171.152 5 N4 6(C ) 2 O6 5(G ) 1 1 1 2.890 151.690 5 N1 7(G ) 2 N3 4(C ) 1 1 1 2.926 157.926 5 N2 7(G ) 2 O2 4(C ) 1 1 1 2.969 166.921 5 N3 8(T ) 2 N1 3(A ) 1 1 1 2.769 140.208 5 N1 9(G ) 2 O2 2(C ) 1 1 1 3.279 138.767 5 N1 9(G ) 2 N3 2(C ) 1 1 1 2.912 158.381 5 N2 9(G ) 2 O2 2(C ) 1 1 1 2.888 161.393 5 N1 10(G ) 2 N3 1(C ) 1 1 1 2.956 166.570 5 N2 10(G ) 2 O2 1(C ) 1 1 1 2.927 174.575 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, 1kkv_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: 10 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: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( G) 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: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) 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: 1kkv_wc.csv Wattos started at: April 20, 2007 11:49:08 AM CDT Wattos stopped at: April 20, 2007 11:49:13 AM CDT Wattos took (#ms): 5028