Read libraries from system resource. Wattos started at: April 20, 2007 11:54:16 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/pdb1tn9.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 39820 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2379 Found number of new bond candidates: 2063 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: 65 Found number of new hydrogen bonds: 65 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 7(ARG) 1 N 6(ASN) 1 1 1 2.669 106.487 5 N 8(GLY) 1 N 9(ARG) 1 1 1 2.665 94.537 5 N 9(ARG) 1 N 8(GLY) 1 1 1 2.665 106.842 5 N 15(GLU) 1 N 14(GLY) 1 1 1 2.776 98.325 5 N 16(SER) 1 O 24(LEU) 1 1 1 2.954 125.655 5 N 20(ASP) 1 N 19(LYS) 1 1 1 2.654 105.035 5 N 21(GLY) 1 N 20(ASP) 1 1 1 2.655 106.722 5 N 22(ARG) 1 N 21(GLY) 1 1 1 2.694 105.149 5 N 31(PHE) 1 N 30(SER) 1 1 1 2.668 105.970 5 N 32(GLY) 1 N 31(PHE) 1 1 1 2.697 102.798 5 N 33(GLU) 1 N 32(GLY) 1 1 1 2.695 102.714 5 N 35(GLN) 1 O 27(TYR) 1 1 1 3.005 126.167 5 N 41(LYS) 1 N 40(TRP) 1 1 1 2.692 102.907 5 N 43(VAL) 1 N 42(LEU) 1 1 1 2.656 101.960 5 N 45(THR) 1 O 43(VAL) 1 1 1 2.694 143.955 5 N 45(THR) 1 N 46(ASP) 1 1 1 2.696 100.469 5 N 46(ASP) 1 N 45(THR) 1 1 1 2.696 102.846 5 N 52(LYS) 1 O 49(PRO) 1 1 1 3.092 152.171 5 N 52(LYS) 1 N 51(GLY) 1 1 1 2.682 105.569 5 N 58(LEU) 1 O 41(LYS) 1 1 1 3.109 148.173 5 N 59(ARG) 1 N 58(LEU) 1 1 1 2.747 98.759 5 N 60(GLU) 1 O 57(SER) 1 1 1 2.708 138.849 5 N 60(GLU) 1 N 59(ARG) 1 1 1 2.737 100.761 5 N 61(LYS) 1 N 60(GLU) 1 1 1 2.766 97.877 5 N 62(ILE) 1 O 58(LEU) 1 1 1 2.671 168.864 5 N 63(ALA) 1 O 59(ARG) 1 1 1 3.017 151.940 5 N 63(ALA) 1 N 62(ILE) 1 1 1 2.819 96.033 5 N 64(GLU) 1 O 61(LYS) 1 1 1 2.814 136.877 5 N 64(GLU) 1 N 63(ALA) 1 1 1 2.736 101.479 5 N 65(LEU) 1 O 62(ILE) 1 1 1 2.722 118.948 5 N 65(LEU) 1 N 64(GLU) 1 1 1 2.726 100.446 5 N 66(GLN) 1 O 62(ILE) 1 1 1 2.932 157.889 5 N 66(GLN) 1 N 65(LEU) 1 1 1 2.780 99.750 5 N 67(LYS) 1 N 66(GLN) 1 1 1 2.776 99.511 5 N1 1(G ) 2 N3 13(C ) 3 1 1 2.942 149.007 5 N2 1(G ) 2 O2 13(C ) 3 1 1 2.629 136.321 5 N2 1(G ) 2 N3 13(C ) 3 1 1 3.074 142.582 5 N6 2(A ) 2 O4 12(T ) 3 1 1 3.194 167.988 5 N1 3(G ) 2 N3 11(C ) 3 1 1 3.014 166.525 5 N2 3(G ) 2 O2 11(C ) 3 1 1 2.825 160.375 5 N3 4(T ) 2 N1 10(A ) 3 1 1 2.918 172.244 5 N6 5(A ) 2 O4 9(T ) 3 1 1 2.827 142.143 5 N1 6(G ) 2 N3 8(C ) 3 1 1 3.020 162.729 5 N2 6(G ) 2 O2 8(C ) 3 1 1 2.944 167.833 5 N3 7(T ) 2 N1 7(A ) 3 1 1 2.686 162.966 5 N6 8(A ) 2 O4 6(T ) 3 1 1 3.157 164.373 5 N6 9(A ) 2 O4 5(T ) 3 1 1 2.949 172.805 5 N6 10(A ) 2 O4 4(T ) 3 1 1 3.154 157.747 5 N3 11(T ) 2 N1 3(A ) 3 1 1 2.882 172.883 5 N3 12(T ) 2 N1 2(A ) 3 1 1 2.827 175.458 5 N4 13(C ) 2 O6 1(G ) 3 1 1 3.118 175.026 5 N1 1(G ) 3 N3 13(C ) 2 1 1 2.953 164.622 5 N2 1(G ) 3 O2 13(C ) 2 1 1 2.669 156.745 5 N6 2(A ) 3 O4 12(T ) 2 1 1 3.176 166.248 5 N6 3(A ) 3 O4 11(T ) 2 1 1 2.767 178.521 5 N3 4(T ) 3 N1 10(A ) 2 1 1 3.005 155.834 5 N3 5(T ) 3 N1 9(A ) 2 1 1 2.770 165.216 5 N3 6(T ) 3 N1 8(A ) 2 1 1 2.689 154.618 5 N6 7(A ) 3 O4 7(T ) 2 1 1 3.199 168.692 5 N4 8(C ) 3 O6 6(G ) 2 1 1 3.000 163.344 5 N3 9(T ) 3 N1 5(A ) 2 1 1 3.021 154.871 5 N6 10(A ) 3 O4 4(T ) 2 1 1 3.145 157.715 5 N4 11(C ) 3 O6 3(G ) 2 1 1 3.087 161.280 5 N3 12(T ) 3 N1 2(A ) 2 1 1 2.686 146.132 5 N4 13(C ) 3 O6 1(G ) 2 1 1 3.145 163.898 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, 1tn9_wc.csv] Trying to match bases to eachother for number of bases: 26 Considering number of hydrogen bonds: 65 Results contains number of sets of co-planar bases: 13 Results: Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 3 Model: 1 Entry: 1 Residue: 2( A) Mol: 2 Model: 1 Entry: 1 Residue: 12( T) Mol: 3 Model: 1 Entry: 1 Residue: 3( G) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 3 Model: 1 Entry: 1 Residue: 4( T) Mol: 2 Model: 1 Entry: 1 Residue: 10( A) Mol: 3 Model: 1 Entry: 1 Residue: 5( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 3 Model: 1 Entry: 1 Residue: 6( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 3 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 7( A) Mol: 3 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 6( T) Mol: 3 Model: 1 Entry: 1 Residue: 9( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( T) Mol: 3 Model: 1 Entry: 1 Residue: 10( A) Mol: 2 Model: 1 Entry: 1 Residue: 4( T) Mol: 3 Model: 1 Entry: 1 Residue: 11( T) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 3 Model: 1 Entry: 1 Residue: 12( T) Mol: 2 Model: 1 Entry: 1 Residue: 2( A) Mol: 3 Model: 1 Entry: 1 Residue: 13( C) Mol: 2 Model: 1 Entry: 1 Residue: 1( G) Mol: 3 Model: 1 Entry: 1 Writing results to file: 1tn9_wc.csv Wattos started at: April 20, 2007 11:54:16 AM CDT Wattos stopped at: April 20, 2007 11:54:26 AM CDT Wattos took (#ms): 10070