Read libraries from system resource. Wattos started at: January 19, 2007 10:18:00 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/pdb1n8x.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 23400 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1460 Found number of new bond candidates: 1263 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: 42 Found number of new hydrogen bonds: 42 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 36(C ) 1 1 1 2.881 161.746 5 N2 1(G ) 1 O2 36(C ) 1 1 1 2.845 146.799 5 N1 2(G ) 1 N3 35(C ) 1 1 1 2.881 159.210 5 N2 2(G ) 1 O2 35(C ) 1 1 1 2.860 151.466 5 N6 3(A ) 1 O4 34(U ) 1 1 1 2.900 167.979 5 N4 4(C ) 1 O6 33(G ) 1 1 1 2.884 164.878 5 N3 5(U ) 1 N1 32(A ) 1 1 1 2.895 167.944 5 N4 6(C ) 1 O6 31(G ) 1 1 1 2.894 172.663 5 N1 7(G ) 1 N3 30(C ) 1 1 1 2.883 166.869 5 N2 7(G ) 1 O2 30(C ) 1 1 1 2.893 166.800 5 N1 8(G ) 1 N1 27(A ) 1 1 1 2.909 158.774 5 N4 9(C ) 1 O6 26(G ) 1 1 1 2.908 174.903 5 N3 10(U ) 1 N1 25(A ) 1 1 1 2.900 174.595 5 N3 11(U ) 1 N1 24(A ) 1 1 1 2.900 171.132 5 N1 12(G ) 1 N3 23(C ) 1 1 1 2.882 166.102 5 N2 12(G ) 1 O2 23(C ) 1 1 1 2.867 153.076 5 N4 13(C ) 1 O6 22(G ) 1 1 1 2.910 174.778 5 N3 14(U ) 1 O6 21(G ) 1 1 1 2.895 166.935 5 N1 15(G ) 1 N3 20(C ) 1 1 1 2.900 166.723 5 N2 15(G ) 1 O2 20(C ) 1 1 1 2.893 171.896 5 N2 16(G ) 1 N7 19(A ) 1 1 1 2.854 147.501 5 N6 19(A ) 1 O2* 16(G ) 1 1 1 2.879 160.157 5 N6 19(A ) 1 N3 16(G ) 1 1 1 3.071 159.852 5 N4 20(C ) 1 O6 15(G ) 1 1 1 2.894 170.697 5 N1 21(G ) 1 O2 14(U ) 1 1 1 2.877 157.928 5 N1 22(G ) 1 N3 13(C ) 1 1 1 2.882 170.293 5 N2 22(G ) 1 O2 13(C ) 1 1 1 2.890 161.548 5 N4 23(C ) 1 O6 12(G ) 1 1 1 2.912 174.638 5 N6 24(A ) 1 O4 11(U ) 1 1 1 2.886 164.489 5 N6 25(A ) 1 O4 10(U ) 1 1 1 2.882 162.221 5 N1 26(G ) 1 N3 9(C ) 1 1 1 2.886 171.412 5 N2 26(G ) 1 O2 9(C ) 1 1 1 2.874 156.553 5 N6 27(A ) 1 O6 8(G ) 1 1 1 2.888 164.532 5 N4 30(C ) 1 O6 7(G ) 1 1 1 2.897 169.623 5 N1 31(G ) 1 N3 6(C ) 1 1 1 2.910 174.963 5 N2 31(G ) 1 O2 6(C ) 1 1 1 2.891 170.029 5 N6 32(A ) 1 O4 5(U ) 1 1 1 2.898 175.462 5 N1 33(G ) 1 N3 4(C ) 1 1 1 2.900 163.084 5 N2 33(G ) 1 O2 4(C ) 1 1 1 2.884 165.267 5 N3 34(U ) 1 N1 3(A ) 1 1 1 2.890 167.008 5 N4 35(C ) 1 O6 2(G ) 1 1 1 2.896 168.331 5 N4 36(C ) 1 O6 1(G ) 1 1 1 2.906 170.222 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, 1n8x_wc.csv] Trying to match bases to eachother for number of bases: 36 Considering number of hydrogen bonds: 42 Results contains number of sets of co-planar bases: 13 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 36( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 35( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 34( U) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 33( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( U) Mol: 1 Model: 1 Entry: 1 Residue: 32( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 31( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 30( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( U) Mol: 1 Model: 1 Entry: 1 Residue: 25( A) Mol: 1 Model: 1 Entry: 1 Residue: 11( U) Mol: 1 Model: 1 Entry: 1 Residue: 24( A) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 23( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 22( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1n8x_wc.csv Wattos started at: January 19, 2007 10:18:00 AM CST Wattos stopped at: January 19, 2007 10:18:08 AM CST Wattos took (#ms): 7662