Read libraries from system resource. Wattos started at: January 19, 2007 10:16:10 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/pdb1ekz.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 78228 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2639 Found number of new bond candidates: 2252 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: 63 Found number of new hydrogen bonds: 63 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 13(VAL) 1 N 12(GLN) 1 1 1 2.814 98.715 5 N 14(HIS) 1 O 10(ILE) 1 1 1 2.893 164.201 5 N 14(HIS) 1 N 13(VAL) 1 1 1 2.798 96.431 5 N 15(GLU) 1 O 11(SER) 1 1 1 2.725 170.879 5 N 15(GLU) 1 N 14(HIS) 1 1 1 2.808 96.851 5 N 16(ILE) 1 O 12(GLN) 1 1 1 2.703 172.670 5 N 17(GLY) 1 O 13(VAL) 1 1 1 2.639 150.753 5 N 18(ILE) 1 O 14(HIS) 1 1 1 2.753 159.418 5 N 25(HIS) 1 O 45(ILE) 1 1 1 3.049 168.812 5 N 27(LYS) 1 O 43(ALA) 1 1 1 2.769 173.281 5 N 42(THR) 1 O 53(GLY) 1 1 1 2.985 126.583 5 N 43(ALA) 1 O 27(LYS) 1 1 1 2.654 151.914 5 N 44(CYS) 1 O 51(THR) 1 1 1 2.691 162.816 5 N 45(ILE) 1 O 25(HIS) 1 1 1 2.730 174.001 5 N 49(ILE) 1 O 46(VAL) 1 1 1 3.127 131.622 5 N 53(GLY) 1 O 42(THR) 1 1 1 2.909 115.057 5 N 67(GLU) 1 O 63(LYS) 1 1 1 2.692 154.905 5 N 68(LYS) 1 O 64(ARG) 1 1 1 3.032 162.586 5 N 68(LYS) 1 N 67(GLU) 1 1 1 2.845 95.478 5 N 69(MET) 1 O 65(ALA) 1 1 1 3.123 165.784 5 N 70(LEU) 1 O 66(ALA) 1 1 1 2.772 149.818 5 N 71(VAL) 1 O 67(GLU) 1 1 1 2.690 168.951 5 N 72(GLU) 1 O 68(LYS) 1 1 1 2.765 151.206 5 N 72(GLU) 1 N 71(VAL) 1 1 1 2.786 100.995 5 N 73(LEU) 1 O 69(MET) 1 1 1 2.685 154.092 5 N 74(GLN) 1 O 70(LEU) 1 1 1 2.679 147.848 5 N 74(GLN) 1 N 73(LEU) 1 1 1 2.762 101.889 5 N 75(LYS) 1 N 74(GLN) 1 1 1 2.676 107.152 5 N1 1(G ) 2 N3 30(C ) 2 1 1 2.720 147.804 5 N2 1(G ) 2 O2 30(C ) 2 1 1 2.764 116.103 5 N1 2(G ) 2 N3 29(C ) 2 1 1 2.837 155.668 5 N2 2(G ) 2 O2 29(C ) 2 1 1 2.721 148.450 5 N6 3(A ) 2 O4 28(U ) 2 1 1 2.693 156.262 5 N4 4(C ) 2 O6 27(G ) 2 1 1 2.845 148.457 5 N6 5(A ) 2 O4 26(U ) 2 1 1 2.640 179.355 5 N1 6(G ) 2 N3 25(C ) 2 1 1 2.808 158.884 5 N2 6(G ) 2 O2 25(C ) 2 1 1 2.636 162.957 5 N4 7(C ) 2 O6 24(G ) 2 1 1 2.765 151.886 5 N3 8(U ) 2 N1 23(A ) 2 1 1 2.791 164.861 5 N1 9(G ) 2 N3 22(C ) 2 1 1 2.786 156.469 5 N2 9(G ) 2 O2 22(C ) 2 1 1 2.713 158.581 5 N3 10(U ) 2 N1 21(A ) 2 1 1 2.787 153.134 5 N4 11(C ) 2 O6 20(G ) 2 1 1 3.025 146.734 5 N4 12(C ) 2 O6 19(G ) 2 1 1 3.009 137.850 5 N4 13(C ) 2 O6 18(G ) 2 1 1 2.882 141.800 5 N1 18(G ) 2 O2 13(C ) 2 1 1 3.166 137.853 5 N1 18(G ) 2 N3 13(C ) 2 1 1 2.809 156.990 5 N2 18(G ) 2 O2 13(C ) 2 1 1 2.762 161.084 5 N1 19(G ) 2 N3 12(C ) 2 1 1 2.693 138.481 5 N2 19(G ) 2 O2 12(C ) 2 1 1 2.680 160.710 5 N1 20(G ) 2 N3 11(C ) 2 1 1 2.875 136.100 5 N2 20(G ) 2 O2 11(C ) 2 1 1 2.765 150.198 5 N6 21(A ) 2 O4 10(U ) 2 1 1 2.747 171.613 5 N4 22(C ) 2 O6 9(G ) 2 1 1 2.744 153.647 5 N1 24(G ) 2 N3 7(C ) 2 1 1 2.842 151.142 5 N2 24(G ) 2 O2 7(C ) 2 1 1 2.819 153.082 5 N4 25(C ) 2 O6 6(G ) 2 1 1 2.862 154.492 5 N3 26(U ) 2 N1 5(A ) 2 1 1 2.800 150.097 5 N1 27(G ) 2 N3 4(C ) 2 1 1 2.878 154.236 5 N2 27(G ) 2 O2 4(C ) 2 1 1 2.793 157.032 5 N3 28(U ) 2 N1 3(A ) 2 1 1 2.755 137.689 5 N4 29(C ) 2 O6 2(G ) 2 1 1 2.982 140.614 5 N4 30(C ) 2 O6 1(G ) 2 1 1 3.063 146.021 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, 1ekz_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 63 Results contains number of sets of co-planar bases: 12 Results: Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Residue: 30( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 29( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 2 Model: 1 Entry: 1 Residue: 28( U) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 27( G) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 2 Model: 1 Entry: 1 Residue: 26( U) Mol: 2 Model: 1 Entry: 1 Residue: 6( G) Mol: 2 Model: 1 Entry: 1 Residue: 25( C) Mol: 2 Model: 1 Entry: 1 Residue: 7( C) Mol: 2 Model: 1 Entry: 1 Residue: 24( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 22( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( U) Mol: 2 Model: 1 Entry: 1 Residue: 21( A) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 2 Model: 1 Entry: 1 Residue: 20( G) Mol: 2 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 19( G) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 2 Model: 1 Entry: 1 Residue: 18( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1ekz_wc.csv Wattos started at: January 19, 2007 10:16:10 AM CST Wattos stopped at: January 19, 2007 10:16:19 AM CST Wattos took (#ms): 9198