Read libraries from system resource. Wattos started at: April 20, 2007 11:55:48 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/pdb2lef.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 28776 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2825 Found number of new bond candidates: 2485 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: 146 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 48(GLU) 1 O 45(SER) 1 1 1 108.558 5 N 48(GLU) 1 OG 45(SER) 1 1 1 161.271 5 N 48(GLU) 1 N 47(GLU) 1 1 1 94.886 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 58(LYS) 1 O 54(GLU) 1 1 1 151.228 5 N 58(LYS) 1 O 55(LEU) 1 1 1 109.249 5 N 58(LYS) 1 N 57(ARG) 1 1 1 97.664 5 Found number of new hydrogen bonds: 146 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 11(MET) 1 O 8(ASN) 1 1 1 3.025 136.435 5 N 11(MET) 1 N 10(PHE) 1 1 1 2.735 102.788 5 N 12(LEU) 1 O 9(ALA) 1 1 1 3.061 124.777 5 N 12(LEU) 1 N 11(MET) 1 1 1 2.757 98.047 5 N 13(TYR) 1 O 9(ALA) 1 1 1 2.954 170.060 5 N 13(TYR) 1 N 12(LEU) 1 1 1 2.805 95.178 5 N 14(MET) 1 O 10(PHE) 1 1 1 2.807 164.124 5 N 14(MET) 1 N 13(TYR) 1 1 1 2.802 94.626 5 N 15(LYS) 1 O 11(MET) 1 1 1 2.881 173.247 5 N 16(GLU) 1 O 12(LEU) 1 1 1 2.846 165.909 5 N 16(GLU) 1 N 15(LYS) 1 1 1 2.861 97.779 5 N 17(MET) 1 O 13(TYR) 1 1 1 2.803 164.363 5 N 18(ARG) 1 O 14(MET) 1 1 1 2.715 150.745 5 N 18(ARG) 1 N 17(MET) 1 1 1 2.850 101.820 5 N 19(ALA) 1 N 18(ARG) 1 1 1 2.840 96.006 5 N 20(ASN) 1 O 17(MET) 1 1 1 2.829 116.826 5 N 20(ASN) 1 N 19(ALA) 1 1 1 2.865 97.255 5 N 21(VAL) 1 O 17(MET) 1 1 1 2.789 161.760 5 N 21(VAL) 1 N 20(ASN) 1 1 1 2.873 95.093 5 N 22(VAL) 1 O 18(ARG) 1 1 1 2.804 169.734 5 N 22(VAL) 1 N 21(VAL) 1 1 1 2.868 94.749 5 N 23(ALA) 1 O 19(ALA) 1 1 1 2.869 157.175 5 N 23(ALA) 1 N 22(VAL) 1 1 1 2.795 96.089 5 N 24(GLU) 1 O 20(ASN) 1 1 1 2.784 162.197 5 N 25(SER) 1 O 21(VAL) 1 1 1 2.768 166.528 5 N 25(SER) 1 N 24(GLU) 1 1 1 2.890 98.413 5 OG 25(SER) 1 O 21(VAL) 1 1 1 2.772 158.977 5 N 27(LEU) 1 OG 25(SER) 1 1 1 3.088 151.084 5 N 27(LEU) 1 N 26(THR) 1 1 1 2.729 101.183 5 N 28(LYS) 1 N 29(GLU) 1 1 1 2.761 98.595 5 N 29(GLU) 1 N 28(LYS) 1 1 1 2.761 98.706 5 N 30(SER) 1 N3 11(G ) 3 1 1 2.969 134.647 5 OG 30(SER) 1 N3 10(A ) 3 1 1 2.681 141.651 5 N 32(ALA) 1 O 29(GLU) 1 1 1 2.992 131.693 5 N 32(ALA) 1 N 31(ALA) 1 1 1 2.876 98.424 5 N 33(ILE) 1 O 29(GLU) 1 1 1 2.940 178.362 5 N 33(ILE) 1 N 32(ALA) 1 1 1 2.825 96.515 5 N 34(ASN) 1 N 33(ILE) 1 1 1 2.830 100.666 5 N 35(GLN) 1 O 32(ALA) 1 1 1 2.972 121.328 5 N 35(GLN) 1 N 34(ASN) 1 1 1 2.765 97.856 5 N 36(ILE) 1 O 32(ALA) 1 1 1 2.867 158.041 5 N 36(ILE) 1 N 35(GLN) 1 1 1 2.784 95.046 5 N 37(LEU) 1 O 33(ILE) 1 1 1 2.843 155.670 5 N 38(GLY) 1 O 34(ASN) 1 1 1 2.847 162.169 5 N 38(GLY) 1 N 37(LEU) 1 1 1 2.848 95.652 5 N 39(ARG) 1 O 35(GLN) 1 1 1 2.818 158.231 5 N 39(ARG) 1 O 36(ILE) 1 1 1 3.006 105.748 5 N 40(ARG) 1 O 36(ILE) 1 1 1 2.770 169.917 5 N 41(TRP) 1 O 37(LEU) 1 1 1 2.824 147.840 5 N 41(TRP) 1 N 40(ARG) 1 1 1 2.736 98.084 5 NE1 41(TRP) 1 OE1 49(GLN) 1 1 1 2.797 141.674 5 N 42(HIS) 1 O 39(ARG) 1 1 1 2.839 148.131 5 N 42(HIS) 1 N 41(TRP) 1 1 1 2.783 101.201 5 ND1 42(HIS) 1 O 38(GLY) 1 1 1 2.866 138.285 5 ND1 42(HIS) 1 O 39(ARG) 1 1 1 3.009 123.854 5 N 43(ALA) 1 O 40(ARG) 1 1 1 2.949 155.626 5 N 43(ALA) 1 N 42(HIS) 1 1 1 2.742 103.557 5 N 44(LEU) 1 O 41(TRP) 1 1 1 2.853 161.511 5 N 44(LEU) 1 N 43(ALA) 1 1 1 2.762 102.274 5 N 45(SER) 1 OE1 48(GLU) 1 1 1 2.833 168.325 5 N 47(GLU) 1 N 46(ARG) 1 1 1 2.820 98.847 5 N 48(GLU) 1 O 45(SER) 1 1 1 2.929 108.558 5 N 48(GLU) 1 OG 45(SER) 1 1 1 3.271 161.271 5 N 48(GLU) 1 N 47(GLU) 1 1 1 2.874 94.886 5 N 49(GLN) 1 O 45(SER) 1 1 1 2.812 166.934 5 N 49(GLN) 1 N 48(GLU) 1 1 1 2.823 96.465 5 N 50(ALA) 1 O 46(ARG) 1 1 1 2.822 170.263 5 N 50(ALA) 1 N 49(GLN) 1 1 1 2.916 92.357 5 N 51(LYS) 1 O 47(GLU) 1 1 1 2.866 163.928 5 N 51(LYS) 1 N 50(ALA) 1 1 1 2.862 96.184 5 N 52(TYR) 1 O 49(GLN) 1 1 1 2.790 144.048 5 N 52(TYR) 1 N 51(LYS) 1 1 1 2.846 98.131 5 OH 52(TYR) 1 OE1 16(GLU) 1 1 1 2.699 169.314 5 N 53(TYR) 1 O 50(ALA) 1 1 1 2.810 139.336 5 N 53(TYR) 1 N 52(TYR) 1 1 1 2.811 101.380 5 N 54(GLU) 1 O 50(ALA) 1 1 1 3.102 168.890 5 N 54(GLU) 1 N 53(TYR) 1 1 1 2.718 96.501 5 N 55(LEU) 1 O 51(LYS) 1 1 1 2.817 174.001 5 N 56(ALA) 1 O 52(TYR) 1 1 1 2.745 161.637 5 N 57(ARG) 1 O 54(GLU) 1 1 1 2.877 107.804 5 N 57(ARG) 1 N 56(ALA) 1 1 1 2.844 92.558 5 N 58(LYS) 1 O 54(GLU) 1 1 1 2.770 151.228 5 N 58(LYS) 1 O 55(LEU) 1 1 1 2.942 109.249 5 N 58(LYS) 1 N 57(ARG) 1 1 1 2.855 97.664 5 N 59(GLU) 1 O 55(LEU) 1 1 1 2.842 172.587 5 N 59(GLU) 1 N 58(LYS) 1 1 1 2.874 94.272 5 N 60(ARG) 1 O 56(ALA) 1 1 1 2.868 157.134 5 N 60(ARG) 1 N 59(GLU) 1 1 1 2.806 98.493 5 N 61(GLN) 1 O 57(ARG) 1 1 1 2.880 160.713 5 N 62(LEU) 1 O 58(LYS) 1 1 1 2.791 164.833 5 N 62(LEU) 1 N 61(GLN) 1 1 1 2.852 94.395 5 N 63(HIS) 1 O 59(GLU) 1 1 1 2.814 175.230 5 N 63(HIS) 1 N 62(LEU) 1 1 1 2.874 93.952 5 N 64(MET) 1 O 61(GLN) 1 1 1 2.947 101.290 5 N 65(GLN) 1 O 62(LEU) 1 1 1 2.844 120.742 5 N 65(GLN) 1 N 64(MET) 1 1 1 2.852 100.217 5 N 66(LEU) 1 O 62(LEU) 1 1 1 2.796 170.213 5 N 66(LEU) 1 N 65(GLN) 1 1 1 2.847 94.089 5 N 67(TYR) 1 O 63(HIS) 1 1 1 2.795 154.136 5 N 67(TYR) 1 N 66(LEU) 1 1 1 2.805 96.408 5 N 70(TRP) 1 O 67(TYR) 1 1 1 2.874 161.990 5 N 75(ASN) 1 N 74(ASP) 1 1 1 2.718 104.152 5 OH 76(TYR) 1 O2 5(T ) 3 1 1 2.760 154.707 5 N 79(LYS) 1 N 78(LYS) 1 1 1 2.881 97.360 5 N 79(LYS) 1 O1P 7(C ) 3 1 1 2.670 149.632 5 N4 1(C ) 2 O6 15(G ) 3 1 1 2.859 168.363 5 N6 2(A ) 2 O4 14(T ) 3 1 1 2.868 165.234 5 N4 3(C ) 2 O6 13(G ) 3 1 1 2.831 160.383 5 N4 4(C ) 2 O6 12(G ) 3 1 1 2.861 161.488 5 N4 5(C ) 2 O6 11(G ) 3 1 1 2.831 165.474 5 N3 6(T ) 2 N1 9(A ) 3 1 1 3.101 122.278 5 N3 6(T ) 2 N1 10(A ) 3 1 1 2.721 137.062 5 N3 7(T ) 2 N1 9(A ) 3 1 1 2.777 151.353 5 N3 8(T ) 2 N1 8(A ) 3 1 1 2.768 171.917 5 N1 9(G ) 2 N3 7(C ) 3 1 1 2.883 176.400 5 N2 9(G ) 2 O2 7(C ) 3 1 1 2.915 173.556 5 N6 10(A ) 2 O4 6(T ) 3 1 1 2.829 173.122 5 N6 11(A ) 2 O4 5(T ) 3 1 1 2.855 169.732 5 N1 12(G ) 2 N3 4(C ) 3 1 1 2.844 166.706 5 N2 12(G ) 2 OH 76(TYR) 1 1 1 2.779 147.703 5 N2 12(G ) 2 O2 4(C ) 3 1 1 2.827 160.814 5 N4 13(C ) 2 O6 3(G ) 3 1 1 2.828 170.225 5 N3 14(T ) 2 N1 2(A ) 3 1 1 2.830 178.232 5 N4 15(C ) 2 O6 1(G ) 3 1 1 2.843 168.545 5 N1 1(G ) 3 N3 15(C ) 2 1 1 2.844 170.322 5 N2 1(G ) 3 O2 15(C ) 2 1 1 2.830 167.202 5 N6 2(A ) 3 O4 14(T ) 2 1 1 2.875 171.050 5 N1 3(G ) 3 N3 13(C ) 2 1 1 2.833 173.063 5 N2 3(G ) 3 O2 13(C ) 2 1 1 2.815 168.540 5 N4 4(C ) 3 O6 12(G ) 2 1 1 2.821 162.206 5 N3 5(T ) 3 N1 11(A ) 2 1 1 2.792 163.360 5 N3 6(T ) 3 N1 10(A ) 2 1 1 2.835 163.980 5 N4 7(C ) 3 O6 9(G ) 2 1 1 2.805 175.412 5 N6 8(A ) 3 O4 8(T ) 2 1 1 2.932 174.007 5 N6 9(A ) 3 O4 7(T ) 2 1 1 3.057 160.196 5 N6 10(A ) 3 O4 6(T ) 2 1 1 3.084 165.242 5 N1 11(G ) 3 O2 5(C ) 2 1 1 3.242 132.171 5 N1 11(G ) 3 N3 5(C ) 2 1 1 2.821 166.990 5 N2 11(G ) 3 O2 5(C ) 2 1 1 2.791 162.470 5 N1 12(G ) 3 N3 4(C ) 2 1 1 2.830 170.196 5 N2 12(G ) 3 O2 4(C ) 2 1 1 2.817 160.403 5 N1 13(G ) 3 N3 3(C ) 2 1 1 2.799 168.485 5 N2 13(G ) 3 O2 3(C ) 2 1 1 2.829 165.761 5 N3 14(T ) 3 N1 2(A ) 2 1 1 2.836 176.328 5 N1 15(G ) 3 N3 1(C ) 2 1 1 2.818 165.325 5 N2 15(G ) 3 O2 1(C ) 2 1 1 2.835 169.177 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, 2lef_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 146 Results contains number of sets of co-planar bases: 15 Results: Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Residue: 15( G) Mol: 3 Model: 1 Entry: 1 Residue: 2( A) Mol: 2 Model: 1 Entry: 1 Residue: 14( T) Mol: 3 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 13( G) Mol: 3 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 3 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 3 Model: 1 Entry: 1 Residue: 6( T) Mol: 2 Model: 1 Entry: 1 Residue: 10( A) Mol: 3 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( A) Mol: 3 Model: 1 Entry: 1 Residue: 8( T) Mol: 2 Model: 1 Entry: 1 Residue: 8( A) Mol: 3 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 7( C) Mol: 3 Model: 1 Entry: 1 Residue: 10( A) Mol: 2 Model: 1 Entry: 1 Residue: 6( T) Mol: 3 Model: 1 Entry: 1 Residue: 11( A) Mol: 2 Model: 1 Entry: 1 Residue: 5( T) Mol: 3 Model: 1 Entry: 1 Residue: 12( G) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 3 Model: 1 Entry: 1 Residue: 13( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 3 Model: 1 Entry: 1 Residue: 14( T) Mol: 2 Model: 1 Entry: 1 Residue: 2( A) Mol: 3 Model: 1 Entry: 1 Residue: 15( C) Mol: 2 Model: 1 Entry: 1 Residue: 1( G) Mol: 3 Model: 1 Entry: 1 Writing results to file: 2lef_wc.csv Wattos started at: April 20, 2007 11:55:48 AM CDT Wattos stopped at: April 20, 2007 11:55:58 AM CDT Wattos took (#ms): 9563