Read libraries from system resource. Wattos started at: January 19, 2007 10:15:35 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/pdb1a60.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 33600 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1739 Found number of new bond candidates: 1505 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: 42 Found number of new hydrogen bonds: 42 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 17(C ) 1 1 1 2.706 161.235 5 N2 1(G ) 1 O2 17(C ) 1 1 1 2.738 169.342 5 N1 2(G ) 1 N3 16(C ) 1 1 1 2.707 171.962 5 N2 2(G ) 1 O2 16(C ) 1 1 1 2.651 177.605 5 N1 3(G ) 1 N3 15(C ) 1 1 1 2.704 162.671 5 N2 3(G ) 1 O2 15(C ) 1 1 1 2.648 156.190 5 N6 4(A ) 1 O4 14(U ) 1 1 1 2.395 143.077 5 N1 5(G ) 1 N3 13(C ) 1 1 1 2.716 162.243 5 N1 5(G ) 1 N4 13(C ) 1 1 1 3.149 130.646 5 N2 5(G ) 1 O2 13(C ) 1 1 1 2.730 157.111 5 N2 5(G ) 1 N3 13(C ) 1 1 1 3.126 137.039 5 N4 13(C ) 1 O6 5(G ) 1 1 1 2.568 156.143 5 N4 13(C ) 1 N1 5(G ) 1 1 1 3.149 134.248 5 N3 14(U ) 1 N1 4(A ) 1 1 1 2.848 167.556 5 N4 15(C ) 1 O6 3(G ) 1 1 1 2.633 160.774 5 N4 16(C ) 1 O6 2(G ) 1 1 1 2.646 168.735 5 N4 17(C ) 1 O6 1(G ) 1 1 1 2.562 159.461 5 N4 18(C ) 1 O6 32(G ) 1 1 1 2.548 159.663 5 N4 19(C ) 1 O6 31(G ) 1 1 1 2.630 155.908 5 N4 20(C ) 1 O6 30(G ) 1 1 1 2.643 158.418 5 N3 25(U ) 1 N1 40(A ) 1 1 1 2.817 150.957 5 N4 26(C ) 1 O6 39(G ) 1 1 1 2.685 163.653 5 N4 27(C ) 1 O6 38(G ) 1 1 1 2.601 163.522 5 N1 28(G ) 1 N3 37(C ) 1 1 1 2.694 168.385 5 N2 28(G ) 1 O2 37(C ) 1 1 1 2.693 176.722 5 N6 29(A ) 1 O4 36(U ) 1 1 1 2.664 159.531 5 N1 30(G ) 1 N3 20(C ) 1 1 1 2.678 159.420 5 N2 30(G ) 1 O2 20(C ) 1 1 1 2.599 153.062 5 N2 30(G ) 1 N3 20(C ) 1 1 1 3.045 137.589 5 N1 31(G ) 1 N3 19(C ) 1 1 1 2.698 156.093 5 N2 31(G ) 1 O2 19(C ) 1 1 1 2.624 148.872 5 N2 31(G ) 1 N6 35(A ) 1 1 1 2.338 109.652 5 N1 32(G ) 1 N3 18(C ) 1 1 1 2.707 162.164 5 N2 32(G ) 1 O2 18(C ) 1 1 1 2.754 170.199 5 N6 35(A ) 1 N2 31(G ) 1 1 1 2.338 117.975 5 N3 36(U ) 1 N1 29(A ) 1 1 1 2.982 173.448 5 N4 37(C ) 1 O6 28(G ) 1 1 1 2.577 160.783 5 N1 38(G ) 1 N3 27(C ) 1 1 1 2.695 167.672 5 N2 38(G ) 1 O2 27(C ) 1 1 1 2.685 174.555 5 N1 39(G ) 1 N3 26(C ) 1 1 1 2.695 161.903 5 N2 39(G ) 1 O2 26(C ) 1 1 1 2.594 154.198 5 N6 40(A ) 1 O4 25(U ) 1 1 1 2.655 150.572 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, 1a60_wc.csv] Trying to match bases to eachother for number of bases: 44 Considering number of hydrogen bonds: 42 Results contains number of sets of co-planar bases: 13 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 14( U) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) Mol: 1 Model: 1 Entry: 1 Residue: 32( G) Mol: 1 Model: 1 Entry: 1 Residue: 19( C) Mol: 1 Model: 1 Entry: 1 Residue: 31( G) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 30( G) Mol: 1 Model: 1 Entry: 1 Residue: 25( U) Mol: 1 Model: 1 Entry: 1 Residue: 40( A) Mol: 1 Model: 1 Entry: 1 Residue: 26( C) Mol: 1 Model: 1 Entry: 1 Residue: 39( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 38( G) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 37( C) Mol: 1 Model: 1 Entry: 1 Residue: 29( A) Mol: 1 Model: 1 Entry: 1 Residue: 36( U) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1a60_wc.csv Wattos started at: January 19, 2007 10:15:35 AM CST Wattos stopped at: January 19, 2007 10:15:44 AM CST Wattos took (#ms): 8475