Read libraries from system resource. Wattos started at: January 19, 2007 10:20:11 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/pdb1yg4.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 905 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1139 Found number of new bond candidates: 976 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: 67 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 2(G ) 1 O2 15(C ) 1 1 1 176.338 5 N2 2(G ) 1 N6 18(A ) 1 1 1 144.093 5 N2 2(G ) 1 N1 18(A ) 1 1 1 134.837 5 WARNING: Got more than two hydrogen bond for this donor (N6). Hydrogen bonds (4) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N6 14(A ) 1 O4 3(U ) 1 1 1 175.574 5 N6 14(A ) 1 O6 4(G ) 1 1 1 99.819 5 N6 14(A ) 1 N4 13(C ) 1 1 1 115.128 5 N6 14(A ) 1 N4 15(C ) 1 1 1 94.372 5 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 18(A ) 1 O2* 2(G ) 1 1 1 135.092 5 N6 18(A ) 1 N2 2(G ) 1 1 1 120.334 5 N6 18(A ) 1 N3 2(G ) 1 1 1 141.657 5 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 22(A ) 1 N2 4(G ) 1 1 1 144.731 5 N6 22(A ) 1 O2 13(C ) 1 1 1 119.922 5 N6 22(A ) 1 N1 24(A ) 1 1 1 90.186 5 WARNING: Got more than two hydrogen bond for this donor (O2*). 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 O2* 23(C ) 1 O2P 7(G ) 1 1 1 114.566 5 O2* 23(C ) 1 O1P 24(A ) 1 1 1 113.700 5 O2* 23(C ) 1 O2P 24(A ) 1 1 1 173.167 5 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 24(A ) 1 N2 5(G ) 1 1 1 101.732 5 N6 24(A ) 1 N3 5(G ) 1 1 1 119.184 5 N6 24(A ) 1 O2 13(C ) 1 1 1 129.131 5 WARNING: Got more than two hydrogen bond for this donor (N4). Hydrogen bonds (4) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 25(C ) 1 N2 5(G ) 1 1 1 144.850 5 N4 25(C ) 1 O4* 13(C ) 1 1 1 122.534 5 N4 25(C ) 1 N1 13(C ) 1 1 1 137.345 5 N4 25(C ) 1 N1 24(A ) 1 1 1 93.306 5 Found number of new hydrogen bonds: 67 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N6 1(A ) 1 O4 16(U ) 1 1 1 2.903 176.767 5 O2* 2(G ) 1 N6 18(A ) 1 1 1 2.748 161.001 5 N1 2(G ) 1 N3 15(C ) 1 1 1 2.925 173.290 5 N2 2(G ) 1 O2 15(C ) 1 1 1 2.837 176.338 5 N2 2(G ) 1 N6 18(A ) 1 1 1 3.268 144.093 5 N2 2(G ) 1 N1 18(A ) 1 1 1 2.943 134.837 5 N3 3(U ) 1 N1 14(A ) 1 1 1 2.825 169.968 5 N1 4(G ) 1 N3 13(C ) 1 1 1 2.933 176.239 5 N2 4(G ) 1 O2 13(C ) 1 1 1 2.863 175.033 5 N2 4(G ) 1 N6 21(A ) 1 1 1 2.834 118.417 5 N1 5(G ) 1 N3 12(C ) 1 1 1 2.924 173.520 5 N2 5(G ) 1 O2 12(C ) 1 1 1 2.844 175.776 5 N2 5(G ) 1 N6 24(A ) 1 1 1 3.024 129.301 5 N3 6(CH ) 1 O6 10(G ) 1 1 1 2.852 128.141 5 N3 6(CH ) 1 N4 26(C ) 1 1 1 3.102 143.213 5 N4 6(CH ) 1 N7 10(G ) 1 1 1 2.876 121.915 5 N4 6(CH ) 1 O6 10(G ) 1 1 1 2.417 134.480 5 N4 8(C ) 1 O6 28(G ) 1 1 1 2.905 178.404 5 N4 9(C ) 1 N3 6(CH ) 1 1 1 2.821 99.841 5 N4 9(C ) 1 O6 27(G ) 1 1 1 2.883 167.131 5 N1 10(G ) 1 O4* 12(C ) 1 1 1 2.780 95.442 5 N1 10(G ) 1 N3 26(C ) 1 1 1 2.929 162.663 5 N2 10(G ) 1 O4* 12(C ) 1 1 1 2.180 96.512 5 N2 10(G ) 1 O2 26(C ) 1 1 1 2.884 172.359 5 O2* 11(A ) 1 O1P 12(C ) 1 1 1 2.262 106.671 5 O2* 12(C ) 1 N3 25(C ) 1 1 1 3.039 121.577 5 N4 12(C ) 1 O6 5(G ) 1 1 1 2.894 174.080 5 N4 12(C ) 1 N9 10(G ) 1 1 1 3.051 103.958 5 N4 13(C ) 1 O6 4(G ) 1 1 1 2.892 179.725 5 N4 13(C ) 1 N6 14(A ) 1 1 1 2.989 100.830 5 N6 14(A ) 1 O4 3(U ) 1 1 1 2.917 175.574 5 N6 14(A ) 1 O6 4(G ) 1 1 1 2.922 99.819 5 N6 14(A ) 1 N4 13(C ) 1 1 1 2.989 115.128 5 N6 14(A ) 1 N4 15(C ) 1 1 1 2.885 94.372 5 N4 15(C ) 1 O6 2(G ) 1 1 1 2.891 172.372 5 N3 16(U ) 1 N1 1(A ) 1 1 1 2.812 178.654 5 O2* 18(A ) 1 O4* 19(A ) 1 1 1 2.823 118.190 5 N6 18(A ) 1 O2* 2(G ) 1 1 1 2.748 135.092 5 N6 18(A ) 1 N2 2(G ) 1 1 1 3.268 120.334 5 N6 18(A ) 1 N3 2(G ) 1 1 1 3.159 141.657 5 O2* 19(A ) 1 O5* 20(A ) 1 1 1 2.115 107.794 5 N6 20(A ) 1 N3 14(A ) 1 1 1 2.835 125.808 5 O2* 21(A ) 1 O5* 22(A ) 1 1 1 3.107 127.798 5 N6 21(A ) 1 N2 4(G ) 1 1 1 2.834 129.326 5 N6 21(A ) 1 N3 4(G ) 1 1 1 2.718 101.047 5 O2* 22(A ) 1 O4* 24(A ) 1 1 1 2.787 92.109 5 N6 22(A ) 1 N2 4(G ) 1 1 1 3.252 144.731 5 N6 22(A ) 1 O2 13(C ) 1 1 1 2.910 119.922 5 N6 22(A ) 1 N1 24(A ) 1 1 1 2.866 90.186 5 O2* 23(C ) 1 O2P 7(G ) 1 1 1 3.049 114.566 5 O2* 23(C ) 1 O1P 24(A ) 1 1 1 2.851 113.700 5 O2* 23(C ) 1 O2P 24(A ) 1 1 1 3.070 173.167 5 N6 24(A ) 1 N2 5(G ) 1 1 1 3.024 101.732 5 N6 24(A ) 1 N3 5(G ) 1 1 1 3.305 119.184 5 N6 24(A ) 1 O2 13(C ) 1 1 1 3.138 129.131 5 O2* 25(C ) 1 O5* 26(C ) 1 1 1 2.964 140.348 5 N4 25(C ) 1 N2 5(G ) 1 1 1 3.329 144.850 5 N4 25(C ) 1 O4* 13(C ) 1 1 1 2.626 122.534 5 N4 25(C ) 1 N1 13(C ) 1 1 1 3.089 137.345 5 N4 25(C ) 1 N1 24(A ) 1 1 1 2.927 93.306 5 O2* 26(C ) 1 O4* 27(G ) 1 1 1 3.253 131.954 5 N4 26(C ) 1 O2 6(CH ) 1 1 1 3.212 144.201 5 N4 26(C ) 1 O6 10(G ) 1 1 1 2.871 157.965 5 N1 27(G ) 1 N3 9(C ) 1 1 1 2.954 168.480 5 N2 27(G ) 1 O2 9(C ) 1 1 1 2.876 176.321 5 N1 28(G ) 1 N3 8(C ) 1 1 1 2.943 177.842 5 N2 28(G ) 1 O2 8(C ) 1 1 1 2.876 172.985 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, 1yg4_wc.csv] Trying to match bases to eachother for number of bases: 27 Considering number of hydrogen bonds: 67 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( A) Mol: 1 Model: 1 Entry: 1 Residue: 16( U) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 14( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 27( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 26( C) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1yg4_wc.csv Wattos started at: January 19, 2007 10:20:11 AM CST Wattos stopped at: January 19, 2007 10:20:14 AM CST Wattos took (#ms): 3005