Read libraries from system resource. Wattos started at: April 20, 2007 11:47:21 AM CDT 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/pdb1fyy.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 797 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 980 Found number of new bond candidates: 860 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: 43 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 4(C ) 2 O6 8(G ) 1 1 1 126.486 5 N4 4(C ) 2 O6 9(G ) 1 1 1 171.133 5 N4 4(C ) 2 N1 9(G ) 1 1 1 127.123 5 Found number of new hydrogen bonds: 43 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 1(T ) 1 N1 12(A ) 2 1 1 2.786 151.973 5 N6 2(A ) 1 O4 11(T ) 2 1 1 2.774 174.490 5 N1 3(G ) 1 O2 10(C ) 2 1 1 3.223 131.148 5 N1 3(G ) 1 N3 10(C ) 2 1 1 2.828 168.757 5 N2 3(G ) 1 O2 10(C ) 2 1 1 2.675 167.561 5 N3 4(T ) 1 N1 9(A ) 2 1 1 2.890 178.158 5 N4 5(C ) 1 O6 8(G ) 2 1 1 2.736 176.527 5 N6 6(A ) 1 O4 7(T ) 2 1 1 2.740 163.085 5 N6 7(+A ) 1 N4 5(C ) 2 1 1 3.136 116.820 5 N6 7(+A ) 1 O4 6(T ) 2 1 1 3.212 148.441 5 N1 8(G ) 1 N3 5(C ) 2 1 1 2.835 173.607 5 N2 8(G ) 1 O2 5(C ) 2 1 1 2.741 170.686 5 N1 9(G ) 1 N3 4(C ) 2 1 1 2.786 159.094 5 N1 9(G ) 1 N4 4(C ) 2 1 1 3.294 131.815 5 N2 9(G ) 1 O2 4(C ) 2 1 1 2.753 167.163 5 N2 9(G ) 1 N3 4(C ) 2 1 1 3.221 130.651 5 N1 10(G ) 1 N3 3(C ) 2 1 1 2.794 159.250 5 N2 10(G ) 1 O2 3(C ) 2 1 1 2.799 172.634 5 N2 10(G ) 1 O2 4(C ) 2 1 1 2.958 113.005 5 N4 11(C ) 1 O6 2(G ) 2 1 1 2.823 170.280 5 O5* 1(T ) 2 O2P 2(G ) 2 1 1 2.472 175.814 5 N3 1(T ) 2 N6 12(A ) 1 1 1 3.256 121.294 5 N3 1(T ) 2 N1 12(A ) 1 1 1 2.937 163.236 5 N1 2(G ) 2 O2 11(C ) 1 1 1 3.317 132.211 5 N1 2(G ) 2 N3 11(C ) 1 1 1 2.866 163.929 5 N2 2(G ) 2 O2 11(C ) 1 1 1 2.745 167.889 5 N4 3(C ) 2 O6 10(G ) 1 1 1 2.716 164.284 5 N4 4(C ) 2 O6 8(G ) 1 1 1 2.885 126.486 5 N4 4(C ) 2 O6 9(G ) 1 1 1 2.849 171.133 5 N4 4(C ) 2 N1 9(G ) 1 1 1 3.294 127.123 5 N4 5(C ) 2 O6 8(G ) 1 1 1 2.779 167.465 5 N3 6(T ) 2 N1 7(+A ) 1 1 1 3.037 177.193 5 N3 7(T ) 2 N1 6(A ) 1 1 1 3.068 147.512 5 N1 8(G ) 2 N3 5(C ) 1 1 1 2.846 175.263 5 N2 8(G ) 2 O2 5(C ) 1 1 1 2.803 176.251 5 N6 9(A ) 2 O4 4(T ) 1 1 1 2.746 173.531 5 N4 10(C ) 2 O6 3(G ) 1 1 1 2.840 176.725 5 N3 11(T ) 2 N1 2(A ) 1 1 1 2.894 174.734 5 N6 12(A ) 2 O4 1(T ) 1 1 1 2.848 169.961 5 O9 1(BP ) 3 O2P 6(A ) 1 1 1 2.451 176.352 5 O8 1(BP ) 3 O3* 5(C ) 1 1 1 3.255 117.545 5 O8 1(BP ) 3 O2P 6(A ) 1 1 1 2.584 176.877 5 O7 1(BP ) 3 O4 6(T ) 2 1 1 2.586 175.147 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, 1fyy_wc.csv] Trying to match bases to eachother for number of bases: 23 Considering number of hydrogen bonds: 43 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( T) Mol: 1 Model: 1 Entry: 1 Residue: 12( A) Mol: 2 Model: 1 Entry: 1 Residue: 2( A) Mol: 1 Model: 1 Entry: 1 Residue: 11( T) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1fyy_wc.csv Wattos started at: April 20, 2007 11:47:21 AM CDT Wattos stopped at: April 20, 2007 11:47:24 AM CDT Wattos took (#ms): 2707