Read libraries from system resource. Wattos started at: January 19, 2007 10:22:02 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/pdb2fe9.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 28560 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1602 Found number of new bond candidates: 1441 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 (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 22(TRP) 1 O 18(ASN) 1 1 1 163.004 5 N 22(TRP) 1 O 19(ILE) 1 1 1 99.075 5 N 22(TRP) 1 N 21(MET) 1 1 1 96.797 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(LYS) 1 O 20(PRO) 1 1 1 130.724 5 N 24(LYS) 1 O 21(MET) 1 1 1 120.495 5 N 24(LYS) 1 N 23(LEU) 1 1 1 101.434 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 43(LEU) 1 O 39(PRO) 1 1 1 143.184 5 N 43(LEU) 1 O 40(TRP) 1 1 1 101.748 5 N 43(LEU) 1 N 42(GLU) 1 1 1 100.630 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 45(TYR) 1 O 42(GLU) 1 1 1 135.833 5 N 45(TYR) 1 O 43(LEU) 1 1 1 95.395 5 N 45(TYR) 1 N 44(ILE) 1 1 1 106.285 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 46(LEU) 1 O 42(GLU) 1 1 1 113.683 5 N 46(LEU) 1 O 43(LEU) 1 1 1 148.055 5 N 46(LEU) 1 N 45(TYR) 1 1 1 105.670 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 53(LYS) 1 O 49(GLU) 1 1 1 158.985 5 N 53(LYS) 1 O 50(THR) 1 1 1 107.078 5 N 53(LYS) 1 N 52(GLU) 1 1 1 97.984 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 54(LYS) 1 O 50(THR) 1 1 1 139.868 5 N 54(LYS) 1 O 51(LEU) 1 1 1 125.980 5 N 54(LYS) 1 N 53(LYS) 1 1 1 100.860 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 65(LEU) 1 O 61(ALA) 1 1 1 143.522 5 N 65(LEU) 1 O 62(ARG) 1 1 1 116.397 5 N 65(LEU) 1 N 64(LYS) 1 1 1 98.630 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 77(GLU) 1 O 73(ILE) 1 1 1 132.867 5 N 77(GLU) 1 O 74(ASP) 1 1 1 119.078 5 N 77(GLU) 1 N 76(LYS) 1 1 1 103.088 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 78(ARG) 1 O 74(ASP) 1 1 1 130.470 5 N 78(ARG) 1 O 75(TYR) 1 1 1 127.625 5 N 78(ARG) 1 N 77(GLU) 1 1 1 103.472 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 N 8(LYS) 1 N 7(PRO) 1 1 1 2.684 106.387 5 N 10(LEU) 1 O 6(ASN) 1 1 1 2.835 169.156 5 N 10(LEU) 1 N 9(SER) 1 1 1 2.770 100.049 5 N 11(THR) 1 N 10(LEU) 1 1 1 2.663 105.722 5 N 12(ASP) 1 N 11(THR) 1 1 1 2.680 104.821 5 N 14(LYS) 1 N 13(PRO) 1 1 1 2.769 103.979 5 N 15(LEU) 1 O 12(ASP) 1 1 1 2.830 127.348 5 N 15(LEU) 1 N 14(LYS) 1 1 1 2.828 94.353 5 N 16(LEU) 1 O 12(ASP) 1 1 1 3.192 168.803 5 N 16(LEU) 1 N 15(LEU) 1 1 1 2.798 97.906 5 N 17(LYS) 1 O 13(PRO) 1 1 1 2.851 159.171 5 N 17(LYS) 1 N 16(LEU) 1 1 1 2.860 95.375 5 N 18(ASN) 1 O 15(LEU) 1 1 1 2.725 118.786 5 N 18(ASN) 1 N 17(LYS) 1 1 1 2.657 104.748 5 N 21(MET) 1 O 18(ASN) 1 1 1 2.620 110.648 5 N 21(MET) 1 N 20(PRO) 1 1 1 2.826 95.688 5 N 22(TRP) 1 O 18(ASN) 1 1 1 2.772 163.004 5 N 22(TRP) 1 O 19(ILE) 1 1 1 2.822 99.075 5 N 22(TRP) 1 N 21(MET) 1 1 1 2.748 96.797 5 N 23(LEU) 1 O 19(ILE) 1 1 1 2.702 142.926 5 N 23(LEU) 1 N 22(TRP) 1 1 1 2.703 100.262 5 N 24(LYS) 1 O 20(PRO) 1 1 1 2.886 130.724 5 N 24(LYS) 1 O 21(MET) 1 1 1 2.785 120.495 5 N 24(LYS) 1 N 23(LEU) 1 1 1 2.703 101.434 5 N 25(SER) 1 N 24(LYS) 1 1 1 2.779 97.825 5 N 26(LEU) 1 O 23(LEU) 1 1 1 2.752 137.613 5 N 26(LEU) 1 N 25(SER) 1 1 1 2.651 107.137 5 N 27(ARG) 1 O 24(LYS) 1 1 1 3.321 155.969 5 N 27(ARG) 1 N 26(LEU) 1 1 1 2.634 108.141 5 N 28(LEU) 1 O 23(LEU) 1 1 1 2.938 153.925 5 N 28(LEU) 1 N 27(ARG) 1 1 1 2.690 105.295 5 N 29(HIS) 1 N 28(LEU) 1 1 1 2.662 104.848 5 N 30(LYS) 1 N 29(HIS) 1 1 1 2.518 107.187 5 N 31(TYR) 1 O 28(LEU) 1 1 1 2.782 147.204 5 N 31(TYR) 1 N 30(LYS) 1 1 1 2.660 100.229 5 N 32(SER) 1 O 29(HIS) 1 1 1 2.789 147.645 5 N 32(SER) 1 N 31(TYR) 1 1 1 2.682 103.115 5 N 33(ASP) 1 N 32(SER) 1 1 1 2.806 96.054 5 N 34(ALA) 1 N 33(ASP) 1 1 1 2.765 100.372 5 N 35(LEU) 1 O 31(TYR) 1 1 1 2.792 134.621 5 N 35(LEU) 1 N 34(ALA) 1 1 1 2.731 103.481 5 N 36(SER) 1 O 32(SER) 1 1 1 2.508 121.751 5 N 36(SER) 1 N 35(LEU) 1 1 1 2.701 106.213 5 N 37(GLY) 1 N 36(SER) 1 1 1 2.809 97.552 5 N 38(THR) 1 N 37(GLY) 1 1 1 2.657 106.815 5 NE1 40(TRP) 1 O 85(ALA) 1 1 1 2.950 167.295 5 N 41(ILE) 1 N 40(TRP) 1 1 1 2.815 95.929 5 N 42(GLU) 1 N 41(ILE) 1 1 1 2.700 103.233 5 N 43(LEU) 1 O 39(PRO) 1 1 1 2.698 143.184 5 N 43(LEU) 1 O 40(TRP) 1 1 1 2.766 101.748 5 N 43(LEU) 1 N 42(GLU) 1 1 1 2.705 100.630 5 N 44(ILE) 1 O 40(TRP) 1 1 1 2.659 154.906 5 N 44(ILE) 1 N 43(LEU) 1 1 1 2.840 92.687 5 N 45(TYR) 1 O 42(GLU) 1 1 1 2.911 135.833 5 N 45(TYR) 1 O 43(LEU) 1 1 1 2.821 95.395 5 N 45(TYR) 1 N 44(ILE) 1 1 1 2.664 106.285 5 N 46(LEU) 1 O 42(GLU) 1 1 1 2.792 113.683 5 N 46(LEU) 1 O 43(LEU) 1 1 1 2.770 148.055 5 N 46(LEU) 1 N 45(TYR) 1 1 1 2.690 105.670 5 N 49(GLU) 1 N 48(ASP) 1 1 1 2.767 99.021 5 N 51(LEU) 1 O 47(ASP) 1 1 1 2.908 178.831 5 N 51(LEU) 1 N 50(THR) 1 1 1 2.817 96.879 5 N 52(GLU) 1 O 49(GLU) 1 1 1 3.029 119.149 5 N 52(GLU) 1 N 51(LEU) 1 1 1 2.771 98.168 5 N 53(LYS) 1 O 49(GLU) 1 1 1 3.123 158.985 5 N 53(LYS) 1 O 50(THR) 1 1 1 2.746 107.078 5 N 53(LYS) 1 N 52(GLU) 1 1 1 2.734 97.984 5 N 54(LYS) 1 O 50(THR) 1 1 1 2.964 139.868 5 N 54(LYS) 1 O 51(LEU) 1 1 1 3.085 125.980 5 N 54(LYS) 1 N 53(LYS) 1 1 1 2.750 100.860 5 N 55(GLY) 1 O 51(LEU) 1 1 1 2.949 176.931 5 N 55(GLY) 1 N 56(VAL) 1 1 1 2.647 101.640 5 N 56(VAL) 1 O 51(LEU) 1 1 1 2.743 126.349 5 N 56(VAL) 1 N 55(GLY) 1 1 1 2.647 105.621 5 N 58(ALA) 1 N 57(LEU) 1 1 1 2.705 105.347 5 N 60(GLY) 1 N 59(LEU) 1 1 1 2.617 103.205 5 N 61(ALA) 1 O 58(ALA) 1 1 1 2.772 115.501 5 N 61(ALA) 1 N 60(GLY) 1 1 1 2.811 98.691 5 N 62(ARG) 1 O 58(ALA) 1 1 1 2.836 160.584 5 N 64(LYS) 1 N 63(ARG) 1 1 1 2.666 103.719 5 N 65(LEU) 1 O 61(ALA) 1 1 1 2.892 143.522 5 N 65(LEU) 1 O 62(ARG) 1 1 1 2.673 116.397 5 N 65(LEU) 1 N 64(LYS) 1 1 1 2.773 98.630 5 N 66(LEU) 1 N 65(LEU) 1 1 1 2.676 103.733 5 N 67(LYS) 1 O 64(LYS) 1 1 1 2.787 155.804 5 N 67(LYS) 1 N 66(LEU) 1 1 1 2.662 104.471 5 N 68(ALA) 1 O 65(LEU) 1 1 1 2.933 119.073 5 N 68(ALA) 1 N 67(LYS) 1 1 1 2.696 100.149 5 N 69(PHE) 1 O 65(LEU) 1 1 1 2.834 145.338 5 N 69(PHE) 1 N 68(ALA) 1 1 1 2.692 102.621 5 N 70(GLY) 1 N 69(PHE) 1 1 1 2.789 100.129 5 N 71(ILE) 1 N 70(GLY) 1 1 1 2.897 95.521 5 N 72(VAL) 1 N 71(ILE) 1 1 1 2.739 101.097 5 N 73(ILE) 1 N 72(VAL) 1 1 1 2.782 97.594 5 N 74(ASP) 1 O 70(GLY) 1 1 1 2.889 166.639 5 N 76(LYS) 1 O 72(VAL) 1 1 1 2.707 135.839 5 N 76(LYS) 1 N 75(TYR) 1 1 1 2.685 101.658 5 N 77(GLU) 1 O 73(ILE) 1 1 1 2.520 132.867 5 N 77(GLU) 1 O 74(ASP) 1 1 1 2.779 119.078 5 N 77(GLU) 1 N 76(LYS) 1 1 1 2.649 103.088 5 N 78(ARG) 1 O 74(ASP) 1 1 1 2.715 130.470 5 N 78(ARG) 1 O 75(TYR) 1 1 1 3.279 127.625 5 N 78(ARG) 1 N 77(GLU) 1 1 1 2.689 103.472 5 N 79(ASP) 1 N 78(ARG) 1 1 1 2.655 106.752 5 N 80(LEU) 1 O 75(TYR) 1 1 1 2.722 146.606 5 N 80(LEU) 1 N 79(ASP) 1 1 1 2.683 103.915 5 N 81(ILE) 1 N 80(LEU) 1 1 1 2.651 106.072 5 N 84(SER) 1 N 83(ARG) 1 1 1 2.634 106.514 5 N 85(ALA) 1 O 82(ASP) 1 1 1 2.909 147.221 5 N 85(ALA) 1 N 84(SER) 1 1 1 2.733 100.221 5 N 86(TYR) 1 N 85(ALA) 1 1 1 2.763 98.677 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, 2fe9_wc.csv] Trying to match bases to eachother for number of bases: 0 Considering number of hydrogen bonds: 111 WARNING: requested less than 1 new rows in getNewRowIdList: 0 Results contains number of sets of co-planar bases: 0 Results: Writing results to file: 2fe9_wc.csv Wattos started at: January 19, 2007 10:22:02 AM CST Wattos stopped at: January 19, 2007 10:22:04 AM CST Wattos took (#ms): 2709