Read libraries from system resource. Wattos started at: April 20, 2007 11:49:34 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/pdb1l1m.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 67640 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 3982 Found number of new bond candidates: 3508 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: 178 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(ARG) 1 O 18(GLN) 1 1 1 144.163 5 N 22(ARG) 1 O 19(THR) 1 1 1 116.362 5 N 22(ARG) 1 N 21(SER) 1 1 1 100.474 5 Found number of new hydrogen bonds: 178 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 6(LEU) 1 O2P 14(C ) 4 1 1 2.961 132.504 5 N 7(TYR) 1 OG1 5(THR) 1 1 1 2.936 146.455 5 N 7(TYR) 1 N 6(LEU) 1 1 1 2.668 105.780 5 N 8(ASP) 1 O 5(THR) 1 1 1 2.996 131.466 5 N 8(ASP) 1 N 7(TYR) 1 1 1 2.705 101.228 5 N 9(VAL) 1 N 8(ASP) 1 1 1 2.720 100.607 5 N 10(ALA) 1 O 6(LEU) 1 1 1 2.981 153.206 5 N 10(ALA) 1 N 9(VAL) 1 1 1 2.755 97.918 5 N 11(GLU) 1 O 7(TYR) 1 1 1 2.905 140.643 5 N 11(GLU) 1 N 10(ALA) 1 1 1 2.714 101.566 5 N 12(TYR) 1 O 8(ASP) 1 1 1 3.096 139.382 5 N 12(TYR) 1 N 11(GLU) 1 1 1 2.746 101.005 5 N 13(ALA) 1 O 9(VAL) 1 1 1 2.859 158.827 5 N 13(ALA) 1 N 12(TYR) 1 1 1 2.783 99.792 5 N 14(GLY) 1 O 10(ALA) 1 1 1 2.865 120.241 5 N 14(GLY) 1 N 13(ALA) 1 1 1 2.657 106.009 5 N 15(VAL) 1 O 10(ALA) 1 1 1 2.789 151.635 5 N 15(VAL) 1 N 14(GLY) 1 1 1 2.721 100.172 5 N 18(GLN) 1 N 17(TYR) 1 1 1 2.664 102.842 5 N 19(THR) 1 O 16(SER) 1 1 1 2.968 120.399 5 N 19(THR) 1 N 18(GLN) 1 1 1 2.716 99.389 5 N 20(VAL) 1 O 16(SER) 1 1 1 3.077 163.324 5 N 20(VAL) 1 N 19(THR) 1 1 1 2.766 96.387 5 N 21(SER) 1 O 17(TYR) 1 1 1 2.954 165.522 5 N 21(SER) 1 N 20(VAL) 1 1 1 2.831 95.757 5 N 22(ARG) 1 O 18(GLN) 1 1 1 2.867 144.163 5 N 22(ARG) 1 O 19(THR) 1 1 1 3.121 116.362 5 N 22(ARG) 1 N 21(SER) 1 1 1 2.754 100.474 5 N 23(VAL) 1 O 20(VAL) 1 1 1 2.959 125.794 5 N 23(VAL) 1 N 22(ARG) 1 1 1 2.705 102.268 5 N 24(VAL) 1 O 20(VAL) 1 1 1 2.858 161.442 5 N 24(VAL) 1 N 23(VAL) 1 1 1 2.751 98.137 5 N 25(ASN) 1 O 21(SER) 1 1 1 2.872 156.625 5 N 26(GLN) 1 N 25(ASN) 1 1 1 2.809 99.400 5 N 34(THR) 1 N 33(LYS) 1 1 1 2.867 94.909 5 N 35(ARG) 1 N 34(THR) 1 1 1 2.768 101.885 5 N 36(GLU) 1 N 35(ARG) 1 1 1 2.840 96.406 5 N 37(LYS) 1 N 36(GLU) 1 1 1 2.700 104.667 5 N 38(VAL) 1 O 34(THR) 1 1 1 2.858 148.387 5 N 38(VAL) 1 N 37(LYS) 1 1 1 2.710 101.181 5 N 39(GLU) 1 N 38(VAL) 1 1 1 2.786 97.870 5 N 40(ALA) 1 N 39(GLU) 1 1 1 2.680 103.114 5 N 41(ALA) 1 O 37(LYS) 1 1 1 2.978 146.285 5 N 41(ALA) 1 N 40(ALA) 1 1 1 2.760 99.170 5 N 42(MET) 1 O 38(VAL) 1 1 1 2.826 162.201 5 N 42(MET) 1 N 41(ALA) 1 1 1 2.780 99.341 5 N 43(ALA) 1 N 42(MET) 1 1 1 2.643 107.404 5 N 44(GLU) 1 O 41(ALA) 1 1 1 3.096 136.719 5 N 44(GLU) 1 N 43(ALA) 1 1 1 2.642 104.351 5 N 46(ASN) 1 N 45(LEU) 1 1 1 2.678 107.314 5 N 47(TYR) 1 O 42(MET) 1 1 1 2.770 170.813 5 OH 47(TYR) 1 O2P 14(C ) 4 1 1 2.960 158.377 5 N 50(ASN) 1 O1P 14(C ) 4 1 1 2.871 173.516 5 ND2 50(ASN) 1 O3* 13(G ) 4 1 1 2.659 143.325 5 N 52(CYS) 1 N 51(ARG) 1 1 1 2.691 103.219 5 N 53(ALA) 1 N 52(CYS) 1 1 1 2.729 99.437 5 N 54(GLN) 1 N 53(ALA) 1 1 1 2.670 101.955 5 N 55(GLN) 1 O 51(ARG) 1 1 1 2.932 153.321 5 N 55(GLN) 1 N 54(GLN) 1 1 1 2.748 97.407 5 N 56(LEU) 1 N 55(GLN) 1 1 1 2.730 100.080 5 N 57(ALA) 1 O 53(ALA) 1 1 1 2.712 166.879 5 N 57(ALA) 1 N 56(LEU) 1 1 1 2.842 95.546 5 N 58(GLY) 1 O 54(GLN) 1 1 1 2.857 146.879 5 N 58(GLY) 1 N 57(ALA) 1 1 1 2.745 100.382 5 N 59(LYS) 1 N 58(GLY) 1 1 1 2.689 104.806 5 N 7(TYR) 2 OG1 5(THR) 2 1 1 3.067 130.376 5 N 7(TYR) 2 N 6(LEU) 2 1 1 2.500 109.105 5 N 8(ASP) 2 OG1 5(THR) 2 1 1 3.029 144.009 5 N 8(ASP) 2 N 7(TYR) 2 1 1 2.722 99.225 5 N 9(VAL) 2 N 8(ASP) 2 1 1 2.745 99.305 5 N 10(ALA) 2 N 9(VAL) 2 1 1 2.799 97.781 5 N 11(GLU) 2 O 7(TYR) 2 1 1 2.937 163.137 5 N 11(GLU) 2 N 10(ALA) 2 1 1 2.810 97.838 5 N 12(TYR) 2 O 8(ASP) 2 1 1 2.977 155.838 5 N 12(TYR) 2 N 11(GLU) 2 1 1 2.814 98.720 5 N 13(ALA) 2 O 9(VAL) 2 1 1 2.940 155.224 5 N 13(ALA) 2 N 12(TYR) 2 1 1 2.764 98.957 5 N 14(GLY) 2 O 10(ALA) 2 1 1 2.829 130.985 5 N 14(GLY) 2 N 13(ALA) 2 1 1 2.699 104.589 5 N 15(VAL) 2 N 14(GLY) 2 1 1 2.682 104.383 5 N 18(GLN) 2 N 17(TYR) 2 1 1 2.679 104.417 5 N 19(THR) 2 O 16(SER) 2 1 1 2.835 135.864 5 N 19(THR) 2 N 18(GLN) 2 1 1 2.673 102.955 5 OG1 19(THR) 2 O2P 6(G ) 4 1 1 2.781 128.369 5 N 20(VAL) 2 N 19(THR) 2 1 1 2.662 102.989 5 OG 21(SER) 2 O2P 15(T ) 3 1 1 2.604 144.107 5 N 22(ARG) 2 O 18(GLN) 2 1 1 2.964 147.335 5 N 22(ARG) 2 N 21(SER) 2 1 1 2.729 100.441 5 N 24(VAL) 2 O 20(VAL) 2 1 1 2.791 159.845 5 N 24(VAL) 2 N 23(VAL) 2 1 1 2.759 101.284 5 N 25(ASN) 2 N 24(VAL) 2 1 1 2.796 100.660 5 N 29(HIS) 2 O2P 4(T ) 4 1 1 2.814 103.454 5 OG 31(SER) 2 O2P 5(T ) 4 1 1 3.018 105.408 5 N 34(THR) 2 N 33(LYS) 2 1 1 2.915 93.199 5 N 35(ARG) 2 N 34(THR) 2 1 1 2.782 100.151 5 N 36(GLU) 2 O 32(ALA) 2 1 1 2.761 164.748 5 N 36(GLU) 2 N 35(ARG) 2 1 1 2.825 97.100 5 N 37(LYS) 2 N 36(GLU) 2 1 1 2.799 99.168 5 N 38(VAL) 2 O 34(THR) 2 1 1 3.022 161.732 5 N 38(VAL) 2 N 37(LYS) 2 1 1 2.812 97.790 5 N 39(GLU) 2 N 38(VAL) 2 1 1 2.791 97.240 5 N 40(ALA) 2 O 36(GLU) 2 1 1 2.945 154.549 5 N 40(ALA) 2 N 39(GLU) 2 1 1 2.801 98.233 5 N 41(ALA) 2 O 37(LYS) 2 1 1 2.936 148.872 5 N 41(ALA) 2 N 40(ALA) 2 1 1 2.757 100.426 5 N 42(MET) 2 O 38(VAL) 2 1 1 3.154 140.051 5 N 42(MET) 2 N 41(ALA) 2 1 1 2.725 102.387 5 N 43(ALA) 2 O 40(ALA) 2 1 1 2.993 147.436 5 N 43(ALA) 2 N 42(MET) 2 1 1 2.701 103.615 5 N 44(GLU) 2 N 43(ALA) 2 1 1 2.713 102.190 5 N 45(LEU) 2 O 41(ALA) 2 1 1 3.053 177.127 5 N 45(LEU) 2 N 44(GLU) 2 1 1 2.854 95.146 5 N 46(ASN) 2 N 45(LEU) 2 1 1 2.652 107.124 5 N 47(TYR) 2 O 42(MET) 2 1 1 2.775 156.477 5 N 52(CYS) 2 N 51(ARG) 2 1 1 2.769 101.248 5 N 54(GLN) 2 O 50(ASN) 2 1 1 2.716 155.202 5 N 54(GLN) 2 N 53(ALA) 2 1 1 2.861 98.913 5 NE2 54(GLN) 2 O1P 14(A ) 3 1 1 2.688 142.923 5 N 55(GLN) 2 N 54(GLN) 2 1 1 2.860 95.783 5 N 56(LEU) 2 N 55(GLN) 2 1 1 2.685 101.637 5 N 57(ALA) 2 O 53(ALA) 2 1 1 2.838 167.757 5 N1 1(G ) 3 N3 23(C ) 4 1 1 2.872 172.816 5 N2 1(G ) 3 O2 23(C ) 4 1 1 2.717 179.056 5 N6 2(A ) 3 O4 22(T ) 4 1 1 2.678 174.201 5 N6 3(A ) 3 O4 21(T ) 4 1 1 2.822 172.627 5 N3 4(T ) 3 N1 20(A ) 4 1 1 2.788 179.338 5 N3 5(T ) 3 N1 19(A ) 4 1 1 2.731 172.681 5 N1 6(G ) 3 N3 18(C ) 4 1 1 2.868 172.610 5 N2 6(G ) 3 O2 18(C ) 4 1 1 2.595 164.176 5 N3 7(T ) 3 N1 17(A ) 4 1 1 2.798 175.700 5 N1 8(G ) 3 N3 16(C ) 4 1 1 2.813 171.985 5 N2 8(G ) 3 O2 16(C ) 4 1 1 2.662 168.689 5 N6 9(A ) 3 O4 15(T ) 4 1 1 2.915 166.467 5 N1 10(G ) 3 O2 14(C ) 4 1 1 3.171 131.670 5 N1 10(G ) 3 N3 14(C ) 4 1 1 2.886 166.052 5 N2 10(G ) 3 O2 14(C ) 4 1 1 2.536 169.609 5 N4 11(C ) 3 N4 12(C ) 4 1 1 2.857 99.312 5 N4 11(C ) 3 O6 13(G ) 4 1 1 2.778 166.543 5 N1 12(G ) 3 N3 12(C ) 4 1 1 2.895 161.421 5 N2 12(G ) 3 O2 12(C ) 4 1 1 3.052 172.496 5 N1 13(G ) 3 N3 11(C ) 4 1 1 2.888 175.232 5 N2 13(G ) 3 O2 11(C ) 4 1 1 2.576 164.977 5 N6 14(A ) 3 O4 10(T ) 4 1 1 2.854 164.692 5 N3 15(T ) 3 N1 9(A ) 4 1 1 2.921 172.599 5 N6 16(A ) 3 O4 8(T ) 4 1 1 2.689 174.248 5 N6 17(A ) 3 O4 7(T ) 4 1 1 2.675 158.898 5 N4 18(C ) 3 O6 6(G ) 4 1 1 2.776 171.180 5 N6 19(A ) 3 O4 5(T ) 4 1 1 2.609 178.625 5 N6 20(A ) 3 O4 4(T ) 4 1 1 2.898 170.124 5 N3 21(T ) 3 N1 3(A ) 4 1 1 2.780 177.773 5 N3 22(T ) 3 N1 2(A ) 4 1 1 2.722 174.516 5 N3 23(T ) 3 N1 1(A ) 4 1 1 2.814 177.603 5 N6 1(A ) 4 O4 23(T ) 3 1 1 2.717 174.968 5 N6 2(A ) 4 O4 22(T ) 3 1 1 2.741 179.115 5 N6 3(A ) 4 O4 21(T ) 3 1 1 2.915 169.361 5 N3 4(T ) 4 N1 20(A ) 3 1 1 2.783 176.859 5 N3 5(T ) 4 N1 19(A ) 3 1 1 2.861 172.024 5 N1 6(G ) 4 N3 18(C ) 3 1 1 2.831 173.935 5 N2 6(G ) 4 O2 18(C ) 3 1 1 2.756 164.040 5 N3 7(T ) 4 N1 17(A ) 3 1 1 2.718 169.875 5 N3 8(T ) 4 N1 16(A ) 3 1 1 2.935 176.429 5 N6 9(A ) 4 O4 15(T ) 3 1 1 2.684 177.716 5 N3 10(T ) 4 N1 14(A ) 3 1 1 2.948 169.605 5 N4 11(C ) 4 O6 13(G ) 3 1 1 3.069 172.463 5 N4 12(C ) 4 O6 12(G ) 3 1 1 2.667 161.602 5 N1 13(G ) 4 N3 11(C ) 3 1 1 2.954 167.988 5 N2 13(G ) 4 O2 11(C ) 3 1 1 3.016 171.889 5 N4 14(C ) 4 OH 7(TYR) 1 1 1 2.818 145.124 5 N4 14(C ) 4 O6 10(G ) 3 1 1 3.115 160.334 5 N3 15(T ) 4 N1 9(A ) 3 1 1 2.837 172.859 5 N4 16(C ) 4 O6 8(G ) 3 1 1 2.846 168.269 5 N6 17(A ) 4 O4 7(T ) 3 1 1 2.853 173.651 5 N4 18(C ) 4 O6 6(G ) 3 1 1 3.023 173.658 5 N6 19(A ) 4 O4 5(T ) 3 1 1 2.668 170.952 5 N6 20(A ) 4 O4 4(T ) 3 1 1 2.950 171.567 5 N3 21(T ) 4 N1 3(A ) 3 1 1 2.734 178.572 5 N3 22(T ) 4 N1 2(A ) 3 1 1 2.707 174.904 5 N4 23(C ) 4 O6 1(G ) 3 1 1 2.902 170.904 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, 1l1m_wc.csv] Trying to match bases to eachother for number of bases: 46 Considering number of hydrogen bonds: 178 Results contains number of sets of co-planar bases: 23 Results: Residue: 1( G) Mol: 3 Model: 1 Entry: 1 Residue: 23( C) Mol: 4 Model: 1 Entry: 1 Residue: 2( A) Mol: 3 Model: 1 Entry: 1 Residue: 22( T) Mol: 4 Model: 1 Entry: 1 Residue: 3( A) Mol: 3 Model: 1 Entry: 1 Residue: 21( T) Mol: 4 Model: 1 Entry: 1 Residue: 4( T) Mol: 3 Model: 1 Entry: 1 Residue: 20( A) Mol: 4 Model: 1 Entry: 1 Residue: 5( T) Mol: 3 Model: 1 Entry: 1 Residue: 19( A) Mol: 4 Model: 1 Entry: 1 Residue: 6( G) Mol: 3 Model: 1 Entry: 1 Residue: 18( C) Mol: 4 Model: 1 Entry: 1 Residue: 7( T) Mol: 3 Model: 1 Entry: 1 Residue: 17( A) Mol: 4 Model: 1 Entry: 1 Residue: 8( G) Mol: 3 Model: 1 Entry: 1 Residue: 16( C) Mol: 4 Model: 1 Entry: 1 Residue: 9( A) Mol: 3 Model: 1 Entry: 1 Residue: 15( T) Mol: 4 Model: 1 Entry: 1 Residue: 10( G) Mol: 3 Model: 1 Entry: 1 Residue: 14( C) Mol: 4 Model: 1 Entry: 1 Residue: 11( C) Mol: 3 Model: 1 Entry: 1 Residue: 13( G) Mol: 4 Model: 1 Entry: 1 Residue: 12( G) Mol: 3 Model: 1 Entry: 1 Residue: 12( C) Mol: 4 Model: 1 Entry: 1 Residue: 13( G) Mol: 3 Model: 1 Entry: 1 Residue: 11( C) Mol: 4 Model: 1 Entry: 1 Residue: 14( A) Mol: 3 Model: 1 Entry: 1 Residue: 10( T) Mol: 4 Model: 1 Entry: 1 Residue: 15( T) Mol: 3 Model: 1 Entry: 1 Residue: 9( A) Mol: 4 Model: 1 Entry: 1 Residue: 16( A) Mol: 3 Model: 1 Entry: 1 Residue: 8( T) Mol: 4 Model: 1 Entry: 1 Residue: 17( A) Mol: 3 Model: 1 Entry: 1 Residue: 7( T) Mol: 4 Model: 1 Entry: 1 Residue: 18( C) Mol: 3 Model: 1 Entry: 1 Residue: 6( G) Mol: 4 Model: 1 Entry: 1 Residue: 19( A) Mol: 3 Model: 1 Entry: 1 Residue: 5( T) Mol: 4 Model: 1 Entry: 1 Residue: 20( A) Mol: 3 Model: 1 Entry: 1 Residue: 4( T) Mol: 4 Model: 1 Entry: 1 Residue: 21( T) Mol: 3 Model: 1 Entry: 1 Residue: 3( A) Mol: 4 Model: 1 Entry: 1 Residue: 22( T) Mol: 3 Model: 1 Entry: 1 Residue: 2( A) Mol: 4 Model: 1 Entry: 1 Residue: 23( T) Mol: 3 Model: 1 Entry: 1 Residue: 1( A) Mol: 4 Model: 1 Entry: 1 Writing results to file: 1l1m_wc.csv Wattos started at: April 20, 2007 11:49:34 AM CDT Wattos stopped at: April 20, 2007 11:49:44 AM CDT Wattos took (#ms): 10503