Read libraries from system resource. Wattos started at: April 20, 2007 11:48:43 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/pdb1jzc.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 419 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 530 Found number of new bond candidates: 451 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: 29 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* 5(C ) 1 O2* 6(A ) 1 1 1 92.086 5 O2* 5(C ) 1 N9 8(G ) 1 1 1 112.334 5 O2* 5(C ) 1 N3 8(G ) 1 1 1 164.380 5 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 9(G ) 1 N1 4(G ) 1 1 1 115.491 5 N2 9(G ) 1 N6 6(A ) 1 1 1 112.391 5 N2 9(G ) 1 O2 10(C ) 1 1 1 139.707 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 12(C ) 1 O6 1(G ) 1 1 1 102.415 5 N4 12(C ) 1 O6 2(G ) 1 1 1 170.689 5 N4 12(C ) 1 N6 11(A ) 1 1 1 106.419 5 Found number of new hydrogen bonds: 29 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 13(C ) 1 1 1 2.780 146.608 5 N2 1(G ) 1 N3 2(G ) 1 1 1 2.881 101.066 5 N2 1(G ) 1 O2 13(C ) 1 1 1 2.882 156.074 5 N1 2(G ) 1 N3 12(C ) 1 1 1 2.860 163.684 5 N2 2(G ) 1 O2 12(C ) 1 1 1 3.108 169.549 5 O2* 3(U ) 1 O4* 4(G ) 1 1 1 3.307 146.072 5 N3 3(U ) 1 N1 2(G ) 1 1 1 2.886 95.062 5 N3 3(U ) 1 N1 11(A ) 1 1 1 2.830 162.119 5 N1 4(G ) 1 N3 10(C ) 1 1 1 2.806 135.753 5 N2 4(G ) 1 O2 10(C ) 1 1 1 2.705 134.364 5 N2 4(G ) 1 N9 11(A ) 1 1 1 3.255 122.944 5 O2* 5(C ) 1 O2* 6(A ) 1 1 1 2.795 92.086 5 O2* 5(C ) 1 N9 8(G ) 1 1 1 3.111 112.334 5 O2* 5(C ) 1 N3 8(G ) 1 1 1 2.868 164.380 5 O2* 6(A ) 1 O2* 5(C ) 1 1 1 2.795 123.074 5 O2* 8(G ) 1 O4* 9(G ) 1 1 1 2.573 155.287 5 N2 8(G ) 1 O2P 6(A ) 1 1 1 2.670 96.867 5 N1 9(G ) 1 N3 5(C ) 1 1 1 2.549 110.416 5 N2 9(G ) 1 N1 4(G ) 1 1 1 2.563 115.491 5 N2 9(G ) 1 N6 6(A ) 1 1 1 3.130 112.391 5 N2 9(G ) 1 O2 10(C ) 1 1 1 2.911 139.707 5 N4 10(C ) 1 O6 4(G ) 1 1 1 2.794 154.483 5 N6 11(A ) 1 O6 2(G ) 1 1 1 2.516 112.609 5 N6 11(A ) 1 O4 3(U ) 1 1 1 2.587 145.281 5 N4 12(C ) 1 O6 1(G ) 1 1 1 3.028 102.415 5 N4 12(C ) 1 O6 2(G ) 1 1 1 2.722 170.689 5 N4 12(C ) 1 N6 11(A ) 1 1 1 3.112 106.419 5 N4 13(C ) 1 O6 1(G ) 1 1 1 2.624 170.840 5 N4 13(C ) 1 N4 12(C ) 1 1 1 2.592 91.674 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, 1jzc_wc.csv] Trying to match bases to eachother for number of bases: 13 Considering number of hydrogen bonds: 29 Results contains number of sets of co-planar bases: 3 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 11( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1jzc_wc.csv Wattos started at: April 20, 2007 11:48:43 AM CDT Wattos stopped at: April 20, 2007 11:48:46 AM CDT Wattos took (#ms): 2735