Read libraries from system resource. Wattos started at: April 20, 2007 11:54:04 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/pdb1skp.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 2792 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 859 Found number of new bond candidates: 751 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: 32 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 5(A ) 1 O4 4(T ) 1 1 1 124.158 5 N6 5(A ) 1 N6 6(A ) 2 1 1 100.151 5 N6 5(A ) 1 O4 7(T ) 2 1 1 169.037 5 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 6(A ) 2 N6 5(A ) 1 1 1 102.834 5 N6 6(A ) 2 O4 6(T ) 1 1 1 155.815 5 N6 6(A ) 2 N4 5(C ) 2 1 1 96.723 5 Found number of new hydrogen bonds: 32 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 11(C ) 2 1 1 2.858 169.796 5 N2 1(G ) 1 O2 11(C ) 2 1 1 2.821 168.866 5 N4 2(C ) 1 O6 10(G ) 2 1 1 2.810 165.595 5 N6 3(A ) 1 O4 9(T ) 2 1 1 2.836 163.639 5 N3 4(T ) 1 N1 8(A ) 2 1 1 2.798 164.652 5 N6 5(A ) 1 O4 4(T ) 1 1 1 2.740 124.158 5 N6 5(A ) 1 N6 6(A ) 2 1 1 2.964 100.151 5 N6 5(A ) 1 O4 7(T ) 2 1 1 2.852 169.037 5 N3 6(T ) 1 N1 6(A ) 2 1 1 3.023 160.414 5 N1 7(G ) 1 N3 5(C ) 2 1 1 2.837 168.025 5 N2 7(G ) 1 O2 5(C ) 2 1 1 2.814 165.868 5 N6 8(A ) 1 O4 4(T ) 2 1 1 2.837 169.517 5 N3 9(T ) 1 N1 3(A ) 2 1 1 2.792 175.705 5 N6 10(A ) 1 O4 2(T ) 2 1 1 3.055 153.540 5 N1 11(G ) 1 N3 1(C ) 2 1 1 2.831 169.513 5 N2 11(G ) 1 O2 1(C ) 2 1 1 2.840 174.452 5 N4 1(C ) 2 O6 11(G ) 1 1 1 2.858 174.560 5 N3 2(T ) 2 N1 10(A ) 1 1 1 2.829 159.677 5 N6 3(A ) 2 O4 9(T ) 1 1 1 2.936 169.697 5 N6 3(A ) 2 O4 2(T ) 2 1 1 2.802 126.583 5 N3 4(T ) 2 N1 8(A ) 1 1 1 2.794 166.586 5 N4 5(C ) 2 O6 7(G ) 1 1 1 2.838 160.792 5 N6 6(A ) 2 N6 5(A ) 1 1 1 2.964 102.834 5 N6 6(A ) 2 O4 6(T ) 1 1 1 2.828 155.815 5 N6 6(A ) 2 N4 5(C ) 2 1 1 2.880 96.723 5 N3 7(T ) 2 N1 5(A ) 1 1 1 2.871 172.391 5 N6 8(A ) 2 O4 4(T ) 1 1 1 2.962 168.883 5 N6 8(A ) 2 O4 7(T ) 2 1 1 2.776 115.290 5 N3 9(T ) 2 N1 3(A ) 1 1 1 2.852 169.282 5 N1 10(G ) 2 N3 2(C ) 1 1 1 2.805 161.286 5 N2 10(G ) 2 O2 2(C ) 1 1 1 2.840 167.023 5 N4 11(C ) 2 O6 1(G ) 1 1 1 2.855 170.820 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, 1skp_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 32 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 9( T) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( T) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 1 Model: 1 Entry: 1 Residue: 3( A) Mol: 2 Model: 1 Entry: 1 Residue: 10( A) Mol: 1 Model: 1 Entry: 1 Residue: 2( T) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1skp_wc.csv Wattos started at: April 20, 2007 11:54:04 AM CDT Wattos stopped at: April 20, 2007 11:54:08 AM CDT Wattos took (#ms): 3155