Read libraries from system resource. Wattos started at: April 20, 2007 11:55:16 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/pdb2glo.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 34940 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2021 Found number of new bond candidates: 1813 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: 116 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 13(GLN) 1 O 9(HIS) 1 1 1 115.094 5 N 13(GLN) 1 O 10(PHE) 1 1 1 122.676 5 N 13(GLN) 1 N 12(LEU) 1 1 1 103.743 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 14(VAL) 1 O 10(PHE) 1 1 1 150.303 5 N 14(VAL) 1 O 11(LYS) 1 1 1 115.299 5 N 14(VAL) 1 N 13(GLN) 1 1 1 101.301 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 19(ARG) 1 O 15(LEU) 1 1 1 140.481 5 N 19(ARG) 1 O 16(GLU) 1 1 1 117.713 5 N 19(ARG) 1 N 18(TYR) 1 1 1 99.041 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 20(ASN) 1 O 16(GLU) 1 1 1 119.659 5 N 20(ASN) 1 O 17(SER) 1 1 1 143.394 5 N 20(ASN) 1 N 19(ARG) 1 1 1 106.731 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 24(CYS) 1 O 21(ASP) 1 1 1 145.079 5 N 24(CYS) 1 N 23(ASP) 1 1 1 100.283 5 N 24(CYS) 1 N 25(LYS) 1 1 1 91.828 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 36(ASN) 1 O 32(ALA) 1 1 1 103.483 5 N 36(ASN) 1 O 33(ARG) 1 1 1 139.920 5 N 36(ASN) 1 N 35(TYR) 1 1 1 108.292 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 47(GLN) 1 O 43(GLN) 1 1 1 134.138 5 N 47(GLN) 1 O 44(LYS) 1 1 1 121.980 5 N 47(GLN) 1 N 46(LEU) 1 1 1 101.021 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 48(CYS) 1 O 45(TRP) 1 1 1 141.706 5 N 48(CYS) 1 O 46(LEU) 1 1 1 96.995 5 N 48(CYS) 1 N 47(GLN) 1 1 1 107.706 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(LEU) 1 O 48(CYS) 1 1 1 137.092 5 N 52(LEU) 1 O 49(GLU) 1 1 1 118.528 5 N 52(LEU) 1 N 51(ASN) 1 1 1 101.002 5 Found number of new hydrogen bonds: 116 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 9(HIS) 1 N 8(PRO) 1 1 1 2.794 98.575 5 N 10(PHE) 1 O 7(THR) 1 1 1 3.063 114.666 5 N 10(PHE) 1 N 9(HIS) 1 1 1 2.756 97.339 5 N 11(LYS) 1 O 7(THR) 1 1 1 2.863 173.096 5 N 11(LYS) 1 N 10(PHE) 1 1 1 2.764 93.880 5 N 12(LEU) 1 O 8(PRO) 1 1 1 2.683 168.839 5 N 12(LEU) 1 N 11(LYS) 1 1 1 2.773 95.213 5 N 13(GLN) 1 O 9(HIS) 1 1 1 2.663 115.094 5 N 13(GLN) 1 O 10(PHE) 1 1 1 2.819 122.676 5 N 13(GLN) 1 N 12(LEU) 1 1 1 2.658 103.743 5 N 14(VAL) 1 O 10(PHE) 1 1 1 2.709 150.303 5 N 14(VAL) 1 O 11(LYS) 1 1 1 3.132 115.299 5 N 14(VAL) 1 N 13(GLN) 1 1 1 2.624 101.301 5 N 15(LEU) 1 O 11(LYS) 1 1 1 2.811 163.424 5 N 15(LEU) 1 N 14(VAL) 1 1 1 2.737 96.179 5 N 16(GLU) 1 O 12(LEU) 1 1 1 2.669 151.245 5 N 16(GLU) 1 N 15(LEU) 1 1 1 2.833 96.678 5 N 17(SER) 1 O 13(GLN) 1 1 1 2.924 161.326 5 N 17(SER) 1 N 16(GLU) 1 1 1 2.878 94.766 5 N 18(TYR) 1 O 14(VAL) 1 1 1 2.650 154.382 5 N 18(TYR) 1 N 17(SER) 1 1 1 2.804 99.380 5 N 19(ARG) 1 O 15(LEU) 1 1 1 2.812 140.481 5 N 19(ARG) 1 O 16(GLU) 1 1 1 3.080 117.713 5 N 19(ARG) 1 N 18(TYR) 1 1 1 2.744 99.041 5 N 20(ASN) 1 O 16(GLU) 1 1 1 2.932 119.659 5 N 20(ASN) 1 O 17(SER) 1 1 1 3.043 143.394 5 N 20(ASN) 1 N 19(ARG) 1 1 1 2.856 106.731 5 N 21(ASP) 1 O 17(SER) 1 1 1 2.641 153.659 5 N 21(ASP) 1 N 20(ASN) 1 1 1 2.768 106.106 5 N 23(ASP) 1 N 22(ASN) 1 1 1 2.678 103.504 5 N 24(CYS) 1 O 21(ASP) 1 1 1 2.916 145.079 5 N 24(CYS) 1 N 23(ASP) 1 1 1 2.823 100.283 5 N 24(CYS) 1 N 25(LYS) 1 1 1 2.742 91.828 5 SG 24(CYS) 1 OD1 21(ASP) 1 1 1 3.316 165.852 5 N 25(LYS) 1 O 21(ASP) 1 1 1 2.604 147.194 5 N 25(LYS) 1 N 24(CYS) 1 1 1 2.742 102.461 5 N 26(GLY) 1 O 18(TYR) 1 1 1 3.077 144.029 5 N 27(ASN) 1 O 24(CYS) 1 1 1 2.606 146.551 5 N 27(ASN) 1 N 26(GLY) 1 1 1 2.706 107.101 5 N 29(ARG) 1 N 28(GLN) 1 1 1 2.868 99.359 5 N 30(ALA) 1 N 29(ARG) 1 1 1 2.840 97.794 5 N 31(THR) 1 N 30(ALA) 1 1 1 2.883 96.568 5 N 32(ALA) 1 O 28(GLN) 1 1 1 3.122 160.515 5 N 32(ALA) 1 N 31(THR) 1 1 1 2.780 99.232 5 N 33(ARG) 1 O 29(ARG) 1 1 1 2.865 143.950 5 N 33(ARG) 1 N 32(ALA) 1 1 1 2.731 99.830 5 N 34(LYS) 1 O 30(ALA) 1 1 1 2.812 162.112 5 N 34(LYS) 1 N 33(ARG) 1 1 1 2.820 98.130 5 N 35(TYR) 1 O 31(THR) 1 1 1 2.850 146.084 5 N 35(TYR) 1 N 34(LYS) 1 1 1 2.764 102.377 5 N 36(ASN) 1 O 32(ALA) 1 1 1 2.670 103.483 5 N 36(ASN) 1 O 33(ARG) 1 1 1 3.203 139.920 5 N 36(ASN) 1 N 35(TYR) 1 1 1 2.638 108.292 5 N 37(ILE) 1 O 32(ALA) 1 1 1 2.666 160.456 5 N 40(ARG) 1 N 39(ARG) 1 1 1 2.733 104.304 5 N 41(GLN) 1 N 40(ARG) 1 1 1 2.723 100.509 5 N 42(ILE) 1 N 41(GLN) 1 1 1 2.901 96.552 5 N 43(GLN) 1 N 42(ILE) 1 1 1 2.702 101.462 5 N 44(LYS) 1 O 40(ARG) 1 1 1 2.679 148.020 5 N 44(LYS) 1 N 43(GLN) 1 1 1 2.793 98.161 5 N 45(TRP) 1 O 41(GLN) 1 1 1 2.643 168.299 5 N 45(TRP) 1 N 44(LYS) 1 1 1 2.868 95.973 5 N 46(LEU) 1 O 42(ILE) 1 1 1 3.089 144.585 5 N 46(LEU) 1 N 45(TRP) 1 1 1 2.637 100.857 5 N 47(GLN) 1 O 43(GLN) 1 1 1 3.257 134.138 5 N 47(GLN) 1 O 44(LYS) 1 1 1 2.724 121.980 5 N 47(GLN) 1 N 46(LEU) 1 1 1 2.695 101.021 5 N 48(CYS) 1 O 45(TRP) 1 1 1 2.797 141.706 5 N 48(CYS) 1 O 46(LEU) 1 1 1 2.934 96.995 5 N 48(CYS) 1 N 47(GLN) 1 1 1 2.581 107.706 5 N 49(GLU) 1 O 45(TRP) 1 1 1 2.393 95.778 5 N 49(GLU) 1 N 48(CYS) 1 1 1 2.791 103.829 5 N 50(SER) 1 N 49(GLU) 1 1 1 2.755 99.370 5 N 51(ASN) 1 O 48(CYS) 1 1 1 2.764 121.283 5 N 51(ASN) 1 N 50(SER) 1 1 1 2.726 100.324 5 N 52(LEU) 1 O 48(CYS) 1 1 1 2.881 137.092 5 N 52(LEU) 1 O 49(GLU) 1 1 1 2.888 118.528 5 N 52(LEU) 1 N 51(ASN) 1 1 1 2.712 101.002 5 N 53(ARG) 1 O 49(GLU) 1 1 1 2.997 158.288 5 N 53(ARG) 1 N 52(LEU) 1 1 1 2.726 97.963 5 N 54(SER) 1 N 53(ARG) 1 1 1 2.865 94.855 5 N 55(SER) 1 O 51(ASN) 1 1 1 2.939 134.073 5 N 55(SER) 1 N 54(SER) 1 1 1 2.701 104.247 5 N 56(VAL) 1 N 55(SER) 1 1 1 2.781 100.233 5 N 57(ALA) 1 N 56(VAL) 1 1 1 2.644 108.176 5 N3 1(T ) 2 N1 12(A ) 3 1 1 2.959 161.576 5 N1 2(G ) 2 N3 11(C ) 3 1 1 2.756 177.951 5 N2 2(G ) 2 O2 11(C ) 3 1 1 2.616 169.367 5 N6 3(A ) 2 O4 10(T ) 3 1 1 3.232 155.013 5 N1 4(G ) 2 N3 9(C ) 3 1 1 2.990 168.743 5 N2 4(G ) 2 O2 9(C ) 3 1 1 2.869 162.151 5 N1 5(G ) 2 N3 8(C ) 3 1 1 3.074 169.100 5 N2 5(G ) 2 O2 8(C ) 3 1 1 3.103 171.097 5 N4 6(C ) 2 O6 7(G ) 3 1 1 3.069 158.385 5 N1 7(G ) 2 N3 6(C ) 3 1 1 2.960 151.360 5 N2 7(G ) 2 O2 6(C ) 3 1 1 2.692 161.779 5 N3 8(T ) 2 N1 5(A ) 3 1 1 3.068 171.357 5 N4 9(C ) 2 O6 4(G ) 3 1 1 2.878 159.548 5 N6 10(A ) 2 O4 3(T ) 3 1 1 2.852 169.029 5 N6 11(A ) 2 O4 2(T ) 3 1 1 3.051 167.115 5 N4 12(C ) 2 O6 1(G ) 3 1 1 3.033 172.492 5 N1 1(G ) 3 N3 12(C ) 2 1 1 2.980 172.211 5 N2 1(G ) 3 O2 12(C ) 2 1 1 2.783 163.635 5 N3 2(T ) 3 N1 11(A ) 2 1 1 2.936 169.848 5 N3 3(T ) 3 N1 10(A ) 2 1 1 2.776 171.238 5 N1 4(G ) 3 N3 9(C ) 2 1 1 2.904 168.098 5 N2 4(G ) 3 O2 9(C ) 2 1 1 2.775 157.697 5 N6 5(A ) 3 O4 8(T ) 2 1 1 3.100 166.047 5 N4 6(C ) 3 O6 7(G ) 2 1 1 3.167 156.976 5 N1 7(G ) 3 N3 6(C ) 2 1 1 3.011 153.472 5 N2 7(G ) 3 O2 6(C ) 2 1 1 2.862 166.823 5 N4 8(C ) 3 O6 5(G ) 2 1 1 3.048 167.019 5 N4 9(C ) 3 O6 4(G ) 2 1 1 3.039 169.364 5 N3 10(T ) 3 N1 3(A ) 2 1 1 2.910 165.037 5 N4 11(C ) 3 O6 2(G ) 2 1 1 2.780 171.293 5 N6 12(A ) 3 O4 1(T ) 2 1 1 3.104 163.467 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, 2glo_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 116 Results contains number of sets of co-planar bases: 12 Results: Residue: 1( T) Mol: 2 Model: 1 Entry: 1 Residue: 12( A) Mol: 3 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 3 Model: 1 Entry: 1 Residue: 3( A) Mol: 2 Model: 1 Entry: 1 Residue: 10( T) Mol: 3 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( C) Mol: 3 Model: 1 Entry: 1 Residue: 5( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 3 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 3 Model: 1 Entry: 1 Residue: 7( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 3 Model: 1 Entry: 1 Residue: 8( T) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 3 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( G) Mol: 3 Model: 1 Entry: 1 Residue: 10( A) Mol: 2 Model: 1 Entry: 1 Residue: 3( T) Mol: 3 Model: 1 Entry: 1 Residue: 11( A) Mol: 2 Model: 1 Entry: 1 Residue: 2( T) Mol: 3 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 1( G) Mol: 3 Model: 1 Entry: 1 Writing results to file: 2glo_wc.csv Wattos started at: April 20, 2007 11:55:16 AM CDT Wattos stopped at: April 20, 2007 11:55:26 AM CDT Wattos took (#ms): 10226