Read libraries from system resource. Wattos started at: January 19, 2007 10:18:37 AM CST 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/pdb1nz1.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 13039 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 925 Found number of new bond candidates: 826 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: 24 Found number of new hydrogen bonds: 24 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 24(C ) 1 1 1 3.142 163.313 5 N2 1(G ) 1 O2 24(C ) 1 1 1 3.202 169.540 5 N1 2(G ) 1 N3 23(C ) 1 1 1 3.005 162.184 5 N2 2(G ) 1 O2 23(C ) 1 1 1 2.797 166.512 5 N3 3(U ) 1 N1 22(A ) 1 1 1 3.086 165.760 5 N3 4(U ) 1 N1 21(A ) 1 1 1 2.919 153.576 5 N4 5(C ) 1 O6 20(G ) 1 1 1 2.812 173.418 5 N4 7(C ) 1 O6 17(G ) 1 1 1 2.793 165.841 5 N4 8(C ) 1 O6 16(G ) 1 1 1 3.149 161.274 5 N3 9(U ) 1 N1 15(A ) 1 1 1 2.986 154.501 5 N2 10(G ) 1 N7 14(A ) 1 1 1 3.193 160.451 5 N6 14(A ) 1 N3 10(G ) 1 1 1 2.562 125.754 5 N6 15(A ) 1 O4 9(U ) 1 1 1 2.761 159.063 5 N1 16(G ) 1 N3 8(C ) 1 1 1 3.034 169.160 5 N2 16(G ) 1 O2 8(C ) 1 1 1 2.818 173.479 5 N1 17(G ) 1 N3 7(C ) 1 1 1 2.898 166.118 5 N2 17(G ) 1 O2 7(C ) 1 1 1 2.907 172.350 5 N6 18(A ) 1 N3 6(C ) 1 1 1 2.777 165.082 5 N1 20(G ) 1 N3 5(C ) 1 1 1 2.822 171.410 5 N2 20(G ) 1 O2 5(C ) 1 1 1 2.719 162.806 5 N6 21(A ) 1 O4 4(U ) 1 1 1 2.820 154.616 5 N6 22(A ) 1 O4 3(U ) 1 1 1 2.710 149.167 5 N4 23(C ) 1 O6 2(G ) 1 1 1 3.112 156.499 5 N4 24(C ) 1 O6 1(G ) 1 1 1 2.978 165.178 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, 1nz1_wc.csv] Trying to match bases to eachother for number of bases: 23 Considering number of hydrogen bonds: 24 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 24( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 22( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( U) Mol: 1 Model: 1 Entry: 1 Residue: 21( A) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( U) Mol: 1 Model: 1 Entry: 1 Residue: 15( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1nz1_wc.csv Wattos started at: January 19, 2007 10:18:37 AM CST Wattos stopped at: January 19, 2007 10:18:42 AM CST Wattos took (#ms): 5109