Read libraries from system resource. Wattos started at: January 19, 2007 10:20:16 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/pdb1ymo.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 29940 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1885 Found number of new bond candidates: 1612 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: 55 WARNING: Got more than two hydrogen bond for this donor (N2). Hydrogen bonds (3) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N2 6(G ) 1 O2 24(C ) 1 1 1 158.688 5 N2 6(G ) 1 N3 24(C ) 1 1 1 141.020 5 N2 6(G ) 1 N1 36(A ) 1 1 1 171.927 5 Found number of new hydrogen bonds: 55 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 3.041 158.540 5 N2 1(G ) 1 O2 29(C ) 1 1 1 3.140 165.370 5 N1 2(G ) 1 N3 28(C ) 1 1 1 2.991 150.533 5 N2 2(G ) 1 O2 28(C ) 1 1 1 2.655 138.633 5 N2 2(G ) 1 N3 28(C ) 1 1 1 3.003 149.643 5 N1 3(G ) 1 N3 27(C ) 1 1 1 2.931 162.633 5 N2 3(G ) 1 O2 27(C ) 1 1 1 2.739 164.526 5 N4 4(C ) 1 O6 26(G ) 1 1 1 2.849 162.167 5 N3 5(U ) 1 N1 25(A ) 1 1 1 3.122 155.336 5 N1 6(G ) 1 N3 24(C ) 1 1 1 2.907 164.042 5 N2 6(G ) 1 O2 24(C ) 1 1 1 2.987 158.688 5 N2 6(G ) 1 N3 24(C ) 1 1 1 3.276 141.020 5 N2 6(G ) 1 N1 36(A ) 1 1 1 3.253 171.927 5 N3 7(U ) 1 N7 37(A ) 1 1 1 2.776 147.077 5 N3 8(U ) 1 N7 38(A ) 1 1 1 2.980 170.939 5 N3 9(U ) 1 N7 39(A ) 1 1 1 2.800 177.367 5 N1 15(G ) 1 N3 46(C ) 1 1 1 3.117 152.349 5 N2 15(G ) 1 O2 46(C ) 1 1 1 3.147 149.642 5 N4 16(C ) 1 O6 45(G ) 1 1 1 2.634 141.088 5 N3 17(U ) 1 N1 44(A ) 1 1 1 3.171 152.162 5 N1 18(G ) 1 N3 43(C ) 1 1 1 2.860 164.922 5 N1 18(G ) 1 N4 43(C ) 1 1 1 3.322 133.735 5 N2 18(G ) 1 O2 43(C ) 1 1 1 2.858 158.816 5 N6 19(A ) 1 O4 42(U ) 1 1 1 2.908 153.778 5 N4 20(C ) 1 O6 41(G ) 1 1 1 2.831 159.769 5 N3 21(U ) 1 N1 40(A ) 1 1 1 3.200 169.173 5 N3 22(U ) 1 N1 39(A ) 1 1 1 2.811 146.556 5 N3 23(U ) 1 N1 38(A ) 1 1 1 2.786 167.866 5 N4 24(C ) 1 O6 6(G ) 1 1 1 2.708 154.690 5 N6 25(A ) 1 O4 5(U ) 1 1 1 3.157 153.626 5 N1 26(G ) 1 N3 4(C ) 1 1 1 2.869 163.602 5 N2 26(G ) 1 O2 4(C ) 1 1 1 2.785 167.906 5 N4 27(C ) 1 O6 3(G ) 1 1 1 3.042 157.096 5 N4 28(C ) 1 O6 2(G ) 1 1 1 3.206 163.754 5 N4 29(C ) 1 O6 1(G ) 1 1 1 2.846 160.922 5 N4 29(C ) 1 N4 28(C ) 1 1 1 2.429 108.791 5 N6 35(A ) 1 O2 5(U ) 1 1 1 2.427 168.788 5 N6 36(A ) 1 O2* 6(G ) 1 1 1 2.375 114.131 5 N6 36(A ) 1 N3 6(G ) 1 1 1 2.633 160.819 5 N6 37(A ) 1 O4 7(U ) 1 1 1 2.597 134.706 5 N6 38(A ) 1 O4 8(U ) 1 1 1 2.752 160.628 5 N6 38(A ) 1 O4 23(U ) 1 1 1 3.236 170.224 5 N6 39(A ) 1 O4 9(U ) 1 1 1 2.848 165.111 5 N6 39(A ) 1 O4 22(U ) 1 1 1 3.204 167.303 5 N6 40(A ) 1 O4 21(U ) 1 1 1 2.808 155.753 5 N1 41(G ) 1 N3 20(C ) 1 1 1 2.933 161.522 5 N2 41(G ) 1 O2 20(C ) 1 1 1 2.909 154.213 5 N3 42(U ) 1 N1 19(A ) 1 1 1 3.185 161.287 5 N4 43(C ) 1 O6 18(G ) 1 1 1 2.731 160.111 5 N4 43(C ) 1 N1 18(G ) 1 1 1 3.322 135.341 5 N6 44(A ) 1 O2* 12(C ) 1 1 1 2.239 112.981 5 N6 44(A ) 1 O4 17(U ) 1 1 1 2.508 117.736 5 N1 45(G ) 1 N3 16(C ) 1 1 1 2.977 160.562 5 N2 45(G ) 1 O2 16(C ) 1 1 1 3.210 162.357 5 N4 46(C ) 1 O6 15(G ) 1 1 1 2.956 152.317 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, 1ymo_wc.csv] Trying to match bases to eachother for number of bases: 47 Considering number of hydrogen bonds: 55 Results contains number of sets of co-planar bases: 15 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: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 46( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 45( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( U) Mol: 1 Model: 1 Entry: 1 Residue: 44( A) Mol: 1 Model: 1 Entry: 1 Residue: 18( G) Mol: 1 Model: 1 Entry: 1 Residue: 43( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( A) Mol: 1 Model: 1 Entry: 1 Residue: 42( U) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 41( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( U) Mol: 1 Model: 1 Entry: 1 Residue: 40( A) Mol: 1 Model: 1 Entry: 1 Residue: 22( U) Mol: 1 Model: 1 Entry: 1 Residue: 39( A) Mol: 1 Model: 1 Entry: 1 Residue: 23( U) Mol: 1 Model: 1 Entry: 1 Residue: 38( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1ymo_wc.csv Wattos started at: January 19, 2007 10:20:16 AM CST Wattos stopped at: January 19, 2007 10:20:25 AM CST Wattos took (#ms): 9101