Read libraries from system resource. Wattos started at: January 19, 2007 10:18:10 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/pdb1na2.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 16974 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1184 Found number of new bond candidates: 1011 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: 40 Found number of new hydrogen bonds: 40 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 29(C ) 1 1 1 2.808 160.476 5 N2 1(G ) 1 O2 29(C ) 1 1 1 2.805 167.411 5 N1 2(G ) 1 N3 28(C ) 1 1 1 2.931 172.192 5 N2 2(G ) 1 O2 28(C ) 1 1 1 2.839 172.442 5 N1 3(G ) 1 N3 27(C ) 1 1 1 3.034 159.779 5 N1 3(G ) 1 N4 27(C ) 1 1 1 3.235 137.793 5 N2 3(G ) 1 O2 27(C ) 1 1 1 3.148 153.522 5 N2 3(G ) 1 N3 27(C ) 1 1 1 3.261 145.832 5 N4 4(C ) 1 O6 26(G ) 1 1 1 2.521 135.714 5 N3 5(U ) 1 N1 25(A ) 1 1 1 3.138 147.866 5 N1 6(G ) 1 N3 24(C ) 1 1 1 2.929 143.731 5 N1 6(G ) 1 N4 24(C ) 1 1 1 3.309 146.488 5 N2 6(G ) 1 O2 24(C ) 1 1 1 2.566 134.039 5 N2 6(G ) 1 N3 24(C ) 1 1 1 2.903 147.748 5 N3 7(U ) 1 N3 23(U ) 1 1 1 3.331 122.895 5 N3 7(U ) 1 O4 23(U ) 1 1 1 2.783 154.063 5 N3 8(U ) 1 O2 22(U ) 1 1 1 2.646 145.761 5 N3 9(U ) 1 O2 21(U ) 1 1 1 3.241 164.069 5 N3 11(U ) 1 N1 19(A ) 1 1 1 3.191 173.079 5 N4 12(C ) 1 O6 18(G ) 1 1 1 2.601 146.302 5 N4 12(C ) 1 N1 18(G ) 1 1 1 3.304 128.992 5 O2* 17(U ) 1 O4 13(U ) 1 1 1 3.260 172.479 5 N1 18(G ) 1 N3 12(C ) 1 1 1 2.743 168.080 5 N1 18(G ) 1 N4 12(C ) 1 1 1 3.304 129.551 5 N2 18(G ) 1 O2 12(C ) 1 1 1 2.770 162.992 5 N6 19(A ) 1 O4 11(U ) 1 1 1 3.064 173.432 5 N4 20(C ) 1 O4 10(U ) 1 1 1 3.218 162.537 5 N3 21(U ) 1 O4 9(U ) 1 1 1 2.697 153.498 5 N3 22(U ) 1 O4 8(U ) 1 1 1 2.974 168.720 5 N3 23(U ) 1 O2 7(U ) 1 1 1 2.792 150.388 5 N3 23(U ) 1 N3 7(U ) 1 1 1 3.331 133.335 5 N4 24(C ) 1 O6 6(G ) 1 1 1 3.188 162.935 5 N4 24(C ) 1 N1 6(G ) 1 1 1 3.309 137.750 5 N6 25(A ) 1 O4 5(U ) 1 1 1 3.130 144.048 5 N1 26(G ) 1 N3 4(C ) 1 1 1 2.826 143.315 5 N2 26(G ) 1 O2 4(C ) 1 1 1 3.194 156.933 5 N4 27(C ) 1 O6 3(G ) 1 1 1 2.862 150.559 5 N4 27(C ) 1 N1 3(G ) 1 1 1 3.235 143.170 5 N4 28(C ) 1 O6 2(G ) 1 1 1 2.912 166.988 5 N4 29(C ) 1 O6 1(G ) 1 1 1 2.732 157.576 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, 1na2_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 40 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 28( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( U) Mol: 1 Model: 1 Entry: 1 Residue: 25( A) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 24( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( U) Mol: 1 Model: 1 Entry: 1 Residue: 19( A) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1na2_wc.csv Wattos started at: January 19, 2007 10:18:10 AM CST Wattos stopped at: January 19, 2007 10:18:16 AM CST Wattos took (#ms): 6279