Read libraries from system resource. Wattos started at: April 20, 2007 11:50:08 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/pdb1lfu.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 44780 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2617 Found number of new bond candidates: 2320 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: 111 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 5(A ) 1 N4 4(C ) 1 1 1 108.917 5 N6 5(A ) 1 O4 10(T ) 2 1 1 172.447 5 N6 5(A ) 1 O6 11(G ) 2 1 1 118.330 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 21(PHE) 3 O 17(LEU) 3 1 1 150.666 5 N 21(PHE) 3 O 18(ASN) 3 1 1 104.320 5 N 21(PHE) 3 N 20(TYR) 3 1 1 100.215 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 23(SER) 3 O 20(TYR) 3 1 1 139.309 5 N 23(SER) 3 O 21(PHE) 3 1 1 116.778 5 N 23(SER) 3 N 22(TYR) 3 1 1 106.140 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 52(TRP) 3 O 48(GLN) 3 1 1 164.374 5 N 52(TRP) 3 O 49(VAL) 3 1 1 103.080 5 N 52(TRP) 3 N 51(ASN) 3 1 1 95.704 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 72(ASN) 3 O 68(GLN) 3 1 1 147.262 5 N 72(ASN) 3 O 69(GLU) 3 1 1 123.270 5 N 72(ASN) 3 N 71(ALA) 3 1 1 97.625 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 73(ILE) 3 O 69(GLU) 3 1 1 148.879 5 N 73(ILE) 3 O 70(GLU) 3 1 1 109.038 5 N 73(ILE) 3 N 72(ASN) 3 1 1 100.993 5 Found number of new hydrogen bonds: 111 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 2(C ) 1 O6 13(G ) 2 1 1 2.930 178.592 5 N1 3(G ) 1 N3 12(C ) 2 1 1 2.981 179.258 5 N2 3(G ) 1 O2 12(C ) 2 1 1 2.822 170.794 5 N4 4(C ) 1 O6 11(G ) 2 1 1 2.930 179.572 5 N6 5(A ) 1 N4 4(C ) 1 1 1 2.866 108.917 5 N6 5(A ) 1 O4 10(T ) 2 1 1 2.727 172.447 5 N6 5(A ) 1 O6 11(G ) 2 1 1 3.141 118.330 5 N3 6(T ) 1 N1 9(A ) 2 1 1 3.006 179.575 5 N1 7(G ) 1 N3 8(C ) 2 1 1 2.988 179.018 5 N2 7(G ) 1 O2 8(C ) 2 1 1 2.781 172.230 5 N6 8(A ) 1 O4 7(T ) 2 1 1 2.723 177.479 5 N3 9(T ) 1 N1 6(A ) 2 1 1 3.108 178.132 5 N3 10(T ) 1 N1 5(A ) 2 1 1 2.619 166.301 5 N1 11(G ) 1 N3 4(C ) 2 1 1 2.964 178.800 5 N2 11(G ) 1 O2 4(C ) 2 1 1 2.859 172.830 5 N4 12(C ) 1 O6 3(G ) 2 1 1 2.924 179.392 5 N1 3(G ) 2 N3 12(C ) 1 1 1 2.967 178.915 5 N2 3(G ) 2 O2 12(C ) 1 1 1 2.875 172.450 5 N4 4(C ) 2 O6 11(G ) 1 1 1 2.930 179.663 5 N6 6(A ) 2 O4 9(T ) 1 1 1 2.597 163.227 5 N3 7(T ) 2 N1 8(A ) 1 1 1 2.918 176.786 5 N4 8(C ) 2 O6 7(G ) 1 1 1 3.056 177.288 5 N6 9(A ) 2 O4 6(T ) 1 1 1 2.719 170.865 5 N3 10(T ) 2 N1 5(A ) 1 1 1 2.983 179.750 5 N1 11(G ) 2 N3 4(C ) 1 1 1 2.943 179.175 5 N2 11(G ) 2 O2 4(C ) 1 1 1 2.827 172.379 5 N4 12(C ) 2 O6 3(G ) 1 1 1 2.997 179.639 5 N1 13(G ) 2 N3 2(C ) 1 1 1 2.947 179.582 5 N2 13(G ) 2 O2 2(C ) 1 1 1 2.834 171.375 5 N 8(ASN) 3 N 7(ARG) 3 1 1 2.925 96.509 5 N 12(GLN) 3 N 11(LYS) 3 1 1 2.720 104.836 5 N 13(ALA) 3 O 10(ASN) 3 1 1 3.031 116.572 5 N 13(ALA) 3 N 12(GLN) 3 1 1 2.829 96.256 5 N 14(THR) 3 O 10(ASN) 3 1 1 3.223 171.029 5 N 14(THR) 3 N 13(ALA) 3 1 1 2.808 99.115 5 N 15(GLU) 3 OG1 14(THR) 3 1 1 2.790 111.749 5 N 16(ILE) 3 O 12(GLN) 3 1 1 3.279 156.908 5 N 16(ILE) 3 N 15(GLU) 3 1 1 2.774 99.630 5 N 17(LEU) 3 O 13(ALA) 3 1 1 2.650 170.265 5 N 18(ASN) 3 O 14(THR) 3 1 1 2.999 166.484 5 N 18(ASN) 3 N 17(LEU) 3 1 1 2.878 96.880 5 N 20(TYR) 3 N 19(GLU) 3 1 1 2.819 97.715 5 N 21(PHE) 3 O 17(LEU) 3 1 1 2.743 150.666 5 N 21(PHE) 3 O 18(ASN) 3 1 1 2.790 104.320 5 N 21(PHE) 3 N 20(TYR) 3 1 1 2.750 100.215 5 N 22(TYR) 3 O 18(ASN) 3 1 1 2.900 164.084 5 N 22(TYR) 3 N 21(PHE) 3 1 1 2.856 95.326 5 N 23(SER) 3 O 20(TYR) 3 1 1 2.863 139.309 5 N 23(SER) 3 O 21(PHE) 3 1 1 2.680 116.778 5 N 23(SER) 3 N 22(TYR) 3 1 1 2.728 106.140 5 N 24(HIS) 3 O 21(PHE) 3 1 1 2.939 147.602 5 N 24(HIS) 3 N 23(SER) 3 1 1 2.677 104.336 5 N 25(LEU) 3 N 24(HIS) 3 1 1 2.761 102.115 5 N 27(ASN) 3 O 24(HIS) 3 1 1 2.568 141.184 5 N 27(ASN) 3 N 26(SER) 3 1 1 2.664 107.864 5 N 33(GLU) 3 N 32(GLU) 3 1 1 2.876 93.778 5 N 34(ALA) 3 O 31(SER) 3 1 1 2.842 109.845 5 N 34(ALA) 3 N 33(GLU) 3 1 1 2.718 101.937 5 N 35(LYS) 3 O 31(SER) 3 1 1 2.679 169.239 5 N 36(GLU) 3 O 32(GLU) 3 1 1 3.217 131.635 5 N 36(GLU) 3 N 35(LYS) 3 1 1 2.666 105.142 5 N 37(GLU) 3 O 33(GLU) 3 1 1 2.694 178.911 5 N 38(LEU) 3 O 34(ALA) 3 1 1 2.614 158.400 5 N 38(LEU) 3 N 37(GLU) 3 1 1 2.825 95.024 5 N 39(ALA) 3 O 35(LYS) 3 1 1 3.014 144.518 5 N 40(LYS) 3 O 36(GLU) 3 1 1 2.850 138.290 5 N 40(LYS) 3 N 39(ALA) 3 1 1 2.762 102.128 5 N 41(LYS) 3 O 37(GLU) 3 1 1 2.642 160.645 5 N 41(LYS) 3 N 40(LYS) 3 1 1 2.732 98.885 5 N 42(SER) 3 O 38(LEU) 3 1 1 2.498 171.553 5 N 42(SER) 3 N 41(LYS) 3 1 1 2.822 97.435 5 N 43(GLY) 3 O 39(ALA) 3 1 1 2.884 137.264 5 N 43(GLY) 3 N 42(SER) 3 1 1 2.878 95.216 5 N 44(ILE) 3 O 39(ALA) 3 1 1 3.057 120.389 5 N 44(ILE) 3 N 43(GLY) 3 1 1 2.649 106.257 5 N 48(GLN) 3 O 45(THR) 3 1 1 2.541 136.179 5 N 48(GLN) 3 N 47(SER) 3 1 1 2.840 100.203 5 N 49(VAL) 3 O 46(VAL) 3 1 1 2.649 129.127 5 N 49(VAL) 3 N 48(GLN) 3 1 1 2.750 99.902 5 N 51(ASN) 3 O 47(SER) 3 1 1 3.248 134.621 5 N 51(ASN) 3 N 50(SER) 3 1 1 2.680 105.837 5 N 52(TRP) 3 O 48(GLN) 3 1 1 2.705 164.374 5 N 52(TRP) 3 O 49(VAL) 3 1 1 2.943 103.080 5 N 52(TRP) 3 N 51(ASN) 3 1 1 2.815 95.704 5 N 53(PHE) 3 O 49(VAL) 3 1 1 2.756 166.366 5 N 56(LYS) 3 O 52(TRP) 3 1 1 3.185 144.685 5 N 58(ILE) 3 N 57(ARG) 3 1 1 2.778 97.143 5 N 60(TYR) 3 O 57(ARG) 3 1 1 2.960 115.550 5 N 60(TYR) 3 N 59(ARG) 3 1 1 2.733 102.270 5 N 62(LYS) 3 N 61(LYS) 3 1 1 2.740 108.536 5 N 63(ASN) 3 O 60(TYR) 3 1 1 2.778 134.236 5 N 63(ASN) 3 N 62(LYS) 3 1 1 2.784 99.435 5 N 64(ILE) 3 N 63(ASN) 3 1 1 2.839 98.927 5 N 66(LYS) 3 O 63(ASN) 3 1 1 2.416 150.518 5 N 66(LYS) 3 N 65(GLY) 3 1 1 2.749 105.849 5 N 67(PHE) 3 O 64(ILE) 3 1 1 2.778 125.570 5 N 67(PHE) 3 N 66(LYS) 3 1 1 2.730 100.115 5 N 68(GLN) 3 N 67(PHE) 3 1 1 2.739 102.041 5 N 70(GLU) 3 N 69(GLU) 3 1 1 2.795 98.647 5 N 71(ALA) 3 O 67(PHE) 3 1 1 2.568 159.926 5 N 71(ALA) 3 N 70(GLU) 3 1 1 2.786 95.757 5 N 72(ASN) 3 O 68(GLN) 3 1 1 3.138 147.262 5 N 72(ASN) 3 O 69(GLU) 3 1 1 3.081 123.270 5 N 72(ASN) 3 N 71(ALA) 3 1 1 2.777 97.625 5 N 73(ILE) 3 O 69(GLU) 3 1 1 2.950 148.879 5 N 73(ILE) 3 O 70(GLU) 3 1 1 2.565 109.038 5 N 73(ILE) 3 N 72(ASN) 3 1 1 2.740 100.993 5 N 74(TYR) 3 O 70(GLU) 3 1 1 2.737 155.313 5 N 75(ALA) 3 O 71(ALA) 3 1 1 2.906 134.161 5 N 75(ALA) 3 N 74(TYR) 3 1 1 2.749 102.263 5 N 77(LYS) 3 N 76(ALA) 3 1 1 2.735 103.407 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, 1lfu_wc.csv] Trying to match bases to eachother for number of bases: 28 Considering number of hydrogen bonds: 111 Results contains number of sets of co-planar bases: 10 Results: Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( G) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 10( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( T) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1lfu_wc.csv Wattos started at: April 20, 2007 11:50:08 AM CDT Wattos stopped at: April 20, 2007 11:50:18 AM CDT Wattos took (#ms): 10239