Read libraries from system resource. Wattos started at: January 19, 2007 10:17:25 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/pdb1lc6.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 30720 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 995 Found number of new bond candidates: 827 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: 28 Found number of new hydrogen bonds: 28 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 3.086 151.911 5 N2 1(G ) 1 O2 24(C ) 1 1 1 2.966 156.152 5 N1 2(G ) 1 N3 23(C ) 1 1 1 2.820 158.635 5 N2 2(G ) 1 O2 23(C ) 1 1 1 2.735 151.124 5 N3 3(U ) 1 N6 22(A ) 1 1 1 3.194 134.975 5 N3 3(U ) 1 N1 22(A ) 1 1 1 2.859 160.258 5 N3 4(U ) 1 N1 21(A ) 1 1 1 3.164 175.696 5 N4 5(C ) 1 O6 20(G ) 1 1 1 2.988 152.832 5 N4 7(C ) 1 O6 17(G ) 1 1 1 2.598 136.921 5 N4 8(C ) 1 O6 16(G ) 1 1 1 3.211 163.521 5 N4 8(C ) 1 N1 16(G ) 1 1 1 3.316 136.733 5 N3 9(U ) 1 N1 15(A ) 1 1 1 2.770 161.127 5 N2 10(G ) 1 N7 14(A ) 1 1 1 3.002 158.773 5 N6 15(A ) 1 O4 9(U ) 1 1 1 3.192 157.221 5 N1 16(G ) 1 N3 8(C ) 1 1 1 2.938 145.800 5 N1 16(G ) 1 N4 8(C ) 1 1 1 3.316 149.596 5 N2 16(G ) 1 O2 8(C ) 1 1 1 2.562 132.443 5 N2 16(G ) 1 N3 8(C ) 1 1 1 2.880 149.289 5 N1 17(G ) 1 N3 7(C ) 1 1 1 2.794 164.661 5 N2 17(G ) 1 O2 7(C ) 1 1 1 2.921 159.382 5 N6 18(A ) 1 N3 6(C ) 1 1 1 2.582 135.459 5 N1 20(G ) 1 N3 5(C ) 1 1 1 2.982 155.937 5 N2 20(G ) 1 O2 5(C ) 1 1 1 2.887 159.940 5 N6 21(A ) 1 O4 4(U ) 1 1 1 2.881 175.191 5 N6 22(A ) 1 N3 3(U ) 1 1 1 3.194 138.196 5 N6 22(A ) 1 O4 3(U ) 1 1 1 2.737 157.134 5 N4 23(C ) 1 O6 2(G ) 1 1 1 2.765 156.496 5 N4 24(C ) 1 O6 1(G ) 1 1 1 3.121 148.659 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, 1lc6_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 28 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: 1lc6_wc.csv Wattos started at: January 19, 2007 10:17:25 AM CST Wattos stopped at: January 19, 2007 10:17:32 AM CST Wattos took (#ms): 7013