Read libraries from system resource. Wattos started at: January 19, 2007 10:22:07 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/pdb2gm0.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 22720 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2807 Found number of new bond candidates: 2452 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: 88 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 35(C ) 1 O4 34(U ) 1 1 1 120.107 5 N4 35(C ) 1 O6 1(G ) 2 1 1 163.096 5 N4 35(C ) 1 N6 2(A ) 2 1 1 102.054 5 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 35(C ) 2 O6 1(G ) 1 1 1 160.452 5 N4 35(C ) 2 N6 2(A ) 1 1 1 100.666 5 N4 35(C ) 2 O4 34(U ) 2 1 1 122.063 5 Found number of new hydrogen bonds: 88 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 35(C ) 2 1 1 2.848 170.416 5 N2 1(G ) 1 O2 35(C ) 2 1 1 2.816 171.815 5 N6 2(A ) 1 O4 34(U ) 2 1 1 2.837 168.410 5 N4 3(C ) 1 O6 33(G ) 2 1 1 2.864 169.834 5 N1 4(G ) 1 N3 32(C ) 2 1 1 2.927 120.389 5 N1 5(G ) 1 N1 29(A ) 2 1 1 3.020 173.136 5 N4 6(C ) 1 O6 28(G ) 2 1 1 2.844 175.267 5 N3 7(U ) 1 N1 27(A ) 2 1 1 2.915 149.676 5 O2* 8(U ) 1 O4* 9(G ) 1 1 1 2.973 115.744 5 N3 8(U ) 1 N1 26(A ) 2 1 1 2.842 155.126 5 N1 9(G ) 1 N3 25(C ) 2 1 1 2.828 161.676 5 N2 9(G ) 1 O2 25(C ) 2 1 1 2.783 153.647 5 N4 10(C ) 1 O6 24(G ) 2 1 1 2.827 163.553 5 N3 11(U ) 1 O6 23(G ) 2 1 1 2.854 151.580 5 N1 12(G ) 1 N3 22(C ) 2 1 1 2.796 151.247 5 N2 12(G ) 1 O2 22(C ) 2 1 1 3.022 166.371 5 N1 15(G ) 1 N3 20(C ) 2 1 1 2.813 153.158 5 N2 15(G ) 1 O2 20(C ) 2 1 1 2.813 168.183 5 N4 16(C ) 1 O6 19(G ) 2 1 1 2.838 156.293 5 O2* 17(G ) 1 O4* 18(C ) 1 1 1 3.116 119.367 5 N1 17(G ) 1 N3 18(C ) 2 1 1 2.875 170.359 5 N2 17(G ) 1 O2 18(C ) 2 1 1 2.843 169.351 5 N4 18(C ) 1 O6 17(G ) 2 1 1 2.837 169.860 5 N1 19(G ) 1 N3 16(C ) 2 1 1 2.819 165.404 5 N2 19(G ) 1 O2 16(C ) 2 1 1 2.787 147.900 5 N4 20(C ) 1 O6 15(G ) 2 1 1 2.859 162.506 5 N6 21(A ) 1 N1 14(A ) 2 1 1 2.812 149.546 5 N4 22(C ) 1 O6 12(G ) 2 1 1 2.643 121.354 5 N1 23(G ) 1 O2 11(U ) 2 1 1 2.813 170.249 5 N1 24(G ) 1 N3 10(C ) 2 1 1 2.885 170.476 5 N2 24(G ) 1 O2 10(C ) 2 1 1 2.824 166.899 5 N4 25(C ) 1 O6 9(G ) 2 1 1 2.815 162.473 5 N6 26(A ) 1 O4 8(U ) 2 1 1 2.789 159.294 5 N6 27(A ) 1 O4 7(U ) 2 1 1 2.790 161.850 5 N1 28(G ) 1 N3 6(C ) 2 1 1 2.817 166.472 5 N2 28(G ) 1 O2 6(C ) 2 1 1 2.926 165.535 5 N6 29(A ) 1 O6 5(G ) 2 1 1 2.877 155.437 5 N4 32(C ) 1 O6 4(G ) 2 1 1 2.741 129.685 5 N1 33(G ) 1 N3 3(C ) 2 1 1 2.834 166.393 5 N2 33(G ) 1 O2 3(C ) 2 1 1 2.758 152.082 5 N3 34(U ) 1 N1 2(A ) 2 1 1 2.858 156.715 5 N4 35(C ) 1 O4 34(U ) 1 1 1 2.827 120.107 5 N4 35(C ) 1 O6 1(G ) 2 1 1 2.832 163.096 5 N4 35(C ) 1 N6 2(A ) 2 1 1 2.882 102.054 5 N1 1(G ) 2 N3 35(C ) 1 1 1 2.858 171.060 5 N2 1(G ) 2 O2 35(C ) 1 1 1 2.819 174.768 5 N6 2(A ) 2 O4 34(U ) 1 1 1 2.835 168.249 5 N4 3(C ) 2 O6 33(G ) 1 1 1 2.855 170.429 5 N1 4(G ) 2 N3 32(C ) 1 1 1 2.863 116.105 5 N1 5(G ) 2 N1 29(A ) 1 1 1 2.975 166.398 5 N4 6(C ) 2 O6 28(G ) 1 1 1 2.894 178.300 5 N3 7(U ) 2 N1 27(A ) 1 1 1 2.908 149.652 5 O2* 8(U ) 2 O4* 9(G ) 2 1 1 2.986 116.562 5 N3 8(U ) 2 N1 26(A ) 1 1 1 2.844 152.126 5 N1 9(G ) 2 N3 25(C ) 1 1 1 2.830 160.067 5 N2 9(G ) 2 O2 25(C ) 1 1 1 2.783 153.207 5 N4 10(C ) 2 O6 24(G ) 1 1 1 2.825 162.643 5 N3 11(U ) 2 O6 23(G ) 1 1 1 2.855 150.905 5 N1 12(G ) 2 N3 22(C ) 1 1 1 2.788 151.537 5 N2 12(G ) 2 O2 22(C ) 1 1 1 3.011 167.131 5 N1 15(G ) 2 N3 20(C ) 1 1 1 2.817 152.667 5 N2 15(G ) 2 O2 20(C ) 1 1 1 2.810 167.504 5 N4 16(C ) 2 O6 19(G ) 1 1 1 2.838 155.724 5 O2* 17(G ) 2 O4* 18(C ) 2 1 1 3.112 119.307 5 N1 17(G ) 2 N3 18(C ) 1 1 1 2.875 169.562 5 N2 17(G ) 2 O2 18(C ) 1 1 1 2.840 169.322 5 N4 18(C ) 2 O6 17(G ) 1 1 1 2.837 170.368 5 N1 19(G ) 2 N3 16(C ) 1 1 1 2.822 165.650 5 N2 19(G ) 2 O2 16(C ) 1 1 1 2.788 148.493 5 N4 20(C ) 2 O6 15(G ) 1 1 1 2.860 162.504 5 N6 21(A ) 2 N1 14(A ) 1 1 1 2.810 149.770 5 N4 22(C ) 2 O6 12(G ) 1 1 1 2.639 121.904 5 N1 23(G ) 2 O2 11(U ) 1 1 1 2.809 170.674 5 N1 24(G ) 2 N3 10(C ) 1 1 1 2.884 169.902 5 N2 24(G ) 2 O2 10(C ) 1 1 1 2.821 166.555 5 N4 25(C ) 2 O6 9(G ) 1 1 1 2.819 161.697 5 N6 26(A ) 2 O4 8(U ) 1 1 1 2.813 162.563 5 N6 27(A ) 2 O4 7(U ) 1 1 1 2.798 163.850 5 N1 28(G ) 2 N3 6(C ) 1 1 1 2.821 174.826 5 N2 28(G ) 2 O2 6(C ) 1 1 1 3.067 156.099 5 N6 29(A ) 2 O6 5(G ) 1 1 1 2.826 169.255 5 N4 32(C ) 2 O6 4(G ) 1 1 1 2.728 135.972 5 N1 33(G ) 2 N3 3(C ) 1 1 1 2.837 166.332 5 N2 33(G ) 2 O2 3(C ) 1 1 1 2.758 152.385 5 N3 34(U ) 2 N1 2(A ) 1 1 1 2.860 157.872 5 N4 35(C ) 2 O6 1(G ) 1 1 1 2.840 160.452 5 N4 35(C ) 2 N6 2(A ) 1 1 1 2.849 100.666 5 N4 35(C ) 2 O4 34(U ) 2 1 1 2.798 122.063 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, 2gm0_wc.csv] Trying to match bases to eachother for number of bases: 70 Considering number of hydrogen bonds: 88 Results contains number of sets of co-planar bases: 24 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 35( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 34( U) Mol: 2 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 33( G) Mol: 2 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 32( C) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 2 Model: 1 Entry: 1 Residue: 7( U) Mol: 1 Model: 1 Entry: 1 Residue: 27( A) Mol: 2 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 26( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 25( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 24( G) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 22( C) Mol: 2 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 2 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) Mol: 2 Model: 1 Entry: 1 Residue: 18( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 2 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 2 Model: 1 Entry: 1 Residue: 22( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 2 Model: 1 Entry: 1 Residue: 24( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 25( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 26( A) Mol: 1 Model: 1 Entry: 1 Residue: 8( U) Mol: 2 Model: 1 Entry: 1 Residue: 27( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( U) Mol: 2 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 32( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 33( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 34( U) Mol: 1 Model: 1 Entry: 1 Residue: 2( A) Mol: 2 Model: 1 Entry: 1 Residue: 35( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 2gm0_wc.csv Wattos started at: January 19, 2007 10:22:07 AM CST Wattos stopped at: January 19, 2007 10:22:15 AM CST Wattos took (#ms): 8333