Read libraries from system resource. Wattos started at: January 19, 2007 10:19:10 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/pdb1r2p.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 10940 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1406 Found number of new bond candidates: 1180 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: 36 Found number of new hydrogen bonds: 36 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 34(C ) 1 1 1 2.839 175.428 5 N2 1(G ) 1 O2 34(C ) 1 1 1 2.752 172.716 5 N6 2(A ) 1 O4 33(U ) 1 1 1 2.670 143.437 5 N1 3(G ) 1 O2 32(U ) 1 1 1 3.114 169.837 5 N4 4(C ) 1 O6 31(G ) 1 1 1 2.776 172.588 5 N4 5(C ) 1 O6 30(G ) 1 1 1 2.580 118.086 5 N1 6(G ) 1 N3 29(C ) 1 1 1 2.713 149.465 5 N2 6(G ) 1 O2 29(C ) 1 1 1 2.676 158.461 5 N3 7(U ) 1 N1 28(A ) 1 1 1 2.509 137.078 5 N6 8(A ) 1 O4 27(U ) 1 1 1 2.583 95.286 5 N1 10(G ) 1 N3 23(C ) 1 1 1 2.621 166.302 5 N2 10(G ) 1 O2 23(C ) 1 1 1 2.965 140.394 5 N4 11(C ) 1 O6 22(G ) 1 1 1 2.811 169.980 5 N1 12(G ) 1 N3 21(C ) 1 1 1 2.911 159.519 5 N2 12(G ) 1 O2 21(C ) 1 1 1 2.687 147.723 5 N2 12(G ) 1 N3 21(C ) 1 1 1 3.118 143.600 5 N6 13(A ) 1 O4 20(U ) 1 1 1 2.668 142.912 5 N3 14(U ) 1 O6 19(G ) 1 1 1 3.008 162.378 5 N2 15(G ) 1 N7 18(A ) 1 1 1 2.728 118.005 5 N6 18(A ) 1 N3 15(G ) 1 1 1 2.801 120.588 5 N1 19(G ) 1 O2 14(U ) 1 1 1 3.082 161.354 5 N3 20(U ) 1 N1 13(A ) 1 1 1 3.017 159.850 5 N4 21(C ) 1 O6 12(G ) 1 1 1 3.034 155.743 5 N1 22(G ) 1 N3 11(C ) 1 1 1 2.791 158.638 5 N2 22(G ) 1 O2 11(C ) 1 1 1 2.781 174.913 5 N4 23(C ) 1 O6 10(G ) 1 1 1 2.829 117.979 5 N3 27(U ) 1 N1 8(A ) 1 1 1 2.761 115.483 5 N6 28(A ) 1 O4 7(U ) 1 1 1 2.811 153.703 5 N4 29(C ) 1 O6 6(G ) 1 1 1 2.717 142.856 5 N1 30(G ) 1 N3 5(C ) 1 1 1 2.646 140.609 5 N2 30(G ) 1 O2 5(C ) 1 1 1 2.721 154.617 5 N1 31(G ) 1 N3 4(C ) 1 1 1 2.823 168.987 5 N2 31(G ) 1 O2 4(C ) 1 1 1 2.767 162.850 5 N3 32(U ) 1 O6 3(G ) 1 1 1 2.883 138.731 5 N3 33(U ) 1 N1 2(A ) 1 1 1 2.653 162.606 5 N4 34(C ) 1 O6 1(G ) 1 1 1 2.811 175.587 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, 1r2p_wc.csv] Trying to match bases to eachother for number of bases: 34 Considering number of hydrogen bonds: 36 Results contains number of sets of co-planar bases: 11 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 34( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 33( U) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 31( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 30( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( U) Mol: 1 Model: 1 Entry: 1 Residue: 28( A) Mol: 1 Model: 1 Entry: 1 Residue: 8( A) Mol: 1 Model: 1 Entry: 1 Residue: 27( U) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 22( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( A) Mol: 1 Model: 1 Entry: 1 Residue: 20( U) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1r2p_wc.csv Wattos started at: January 19, 2007 10:19:10 AM CST Wattos stopped at: January 19, 2007 10:19:17 AM CST Wattos took (#ms): 6326