Read libraries from system resource. Wattos started at: April 20, 2007 11:53:14 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/pdb1ql5.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 632 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 746 Found number of new bond candidates: 681 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: 30 Found number of new hydrogen bonds: 30 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O5* 1(C ) 1 O1P 2(G ) 1 1 1 2.548 173.236 5 N4 1(C ) 1 O6 10(G ) 2 1 1 2.799 176.810 5 N1 2(G ) 1 N3 9(C ) 2 1 1 2.940 170.321 5 N2 2(G ) 1 O2 9(C ) 2 1 1 2.862 164.196 5 N4 3(C ) 1 O6 8(G ) 2 1 1 2.725 177.281 5 N6 4(A ) 1 O4 7(T ) 2 1 1 2.833 169.718 5 N3 5(+T ) 1 N1 6(A ) 2 1 1 2.912 149.337 5 N3 6(+T ) 1 O4 5(T ) 2 1 1 3.031 130.253 5 N6 7(A ) 1 O4 4(T ) 2 1 1 2.951 176.026 5 N4 8(C ) 1 O6 3(G ) 2 1 1 2.763 177.100 5 N1 9(G ) 1 N3 2(C ) 2 1 1 2.961 162.561 5 N2 9(G ) 1 O4* 10(C ) 1 1 1 3.051 129.963 5 N2 9(G ) 1 O2 2(C ) 2 1 1 2.984 158.992 5 N4 10(C ) 1 O6 1(G ) 2 1 1 2.802 177.243 5 N1 1(G ) 2 N3 10(C ) 1 1 1 2.922 166.920 5 N2 1(G ) 2 O2 10(C ) 1 1 1 2.843 176.540 5 N4 2(C ) 2 O6 9(G ) 1 1 1 2.750 163.422 5 N1 3(G ) 2 N3 8(C ) 1 1 1 2.890 172.456 5 N2 3(G ) 2 O2 8(C ) 1 1 1 2.916 164.379 5 N3 4(T ) 2 N1 7(A ) 1 1 1 2.874 174.860 5 N3 5(T ) 2 O2 6(+T ) 1 1 1 3.076 134.437 5 N3 5(T ) 2 N1 6(A ) 2 1 1 3.318 135.671 5 N6 6(A ) 2 O4 5(+T ) 1 1 1 3.124 165.358 5 N6 6(A ) 2 O4 5(T ) 2 1 1 3.053 109.478 5 N3 7(T ) 2 N1 4(A ) 1 1 1 2.909 169.995 5 N1 8(G ) 2 N3 3(C ) 1 1 1 2.900 175.244 5 N2 8(G ) 2 O2 3(C ) 1 1 1 2.929 177.324 5 N4 9(C ) 2 O6 2(G ) 1 1 1 2.870 153.561 5 N1 10(G ) 2 N3 1(C ) 1 1 1 2.903 170.651 5 N2 10(G ) 2 O2 1(C ) 1 1 1 2.801 174.692 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, 1ql5_wc.csv] Trying to match bases to eachother for number of bases: 18 Considering number of hydrogen bonds: 30 WARNING: Ignoring potential pair between consequetive bases: Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( T) Mol: 2 Model: 1 Entry: 1 WARNING: Ignoring potential pair between consequetive bases: Residue: 5( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 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( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 2 Model: 1 Entry: 1 Residue: 4( 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: 4( T) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) 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( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1ql5_wc.csv Wattos started at: April 20, 2007 11:53:14 AM CDT Wattos stopped at: April 20, 2007 11:53:16 AM CDT Wattos took (#ms): 2330