Read libraries from system resource. Wattos started at: April 20, 2007 11:51:55 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/pdb1nk2.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 47160 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2832 Found number of new bond candidates: 2451 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: 105 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(LEU) 1 O 20(GLN) 1 1 1 148.103 5 N 24(LEU) 1 O 21(THR) 1 1 1 110.592 5 N 24(LEU) 1 N 23(GLU) 1 1 1 95.990 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 29(ARG) 1 O 25(GLU) 1 1 1 146.872 5 N 29(ARG) 1 O 26(ARG) 1 1 1 116.202 5 N 29(ARG) 1 N 28(PHE) 1 1 1 99.539 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 31(GLN) 1 O 27(ARG) 1 1 1 131.630 5 N 31(GLN) 1 O 28(PHE) 1 1 1 117.007 5 N 31(GLN) 1 N 30(GLN) 1 1 1 102.160 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(ALA) 1 O 39(ARG) 1 1 1 149.145 5 N 43(ALA) 1 O 40(GLU) 1 1 1 100.943 5 N 43(ALA) 1 N 42(LEU) 1 1 1 99.851 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(LEU) 1 O 41(HIS) 1 1 1 119.423 5 N 45(LEU) 1 O 42(LEU) 1 1 1 132.730 5 N 45(LEU) 1 N 44(SER) 1 1 1 98.944 5 Found number of new hydrogen bonds: 105 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 3(ASP) 1 N 4(GLY) 1 1 1 2.723 96.365 5 N 4(GLY) 1 N 3(ASP) 1 1 1 2.723 99.836 5 N 7(ASN) 1 O 5(LEU) 1 1 1 2.868 116.087 5 NH2 13(ARG) 1 O2 5(T ) 2 1 1 3.009 166.236 5 N 19(ALA) 1 N 18(LYS) 1 1 1 2.708 101.223 5 N 20(GLN) 1 O 17(THR) 1 1 1 2.597 95.287 5 N 21(THR) 1 O 17(THR) 1 1 1 2.479 163.116 5 N 21(THR) 1 N 20(GLN) 1 1 1 2.853 93.700 5 N 22(TYR) 1 O 18(LYS) 1 1 1 2.454 155.964 5 N 22(TYR) 1 N 21(THR) 1 1 1 2.877 91.782 5 N 23(GLU) 1 O 19(ALA) 1 1 1 2.845 161.965 5 N 23(GLU) 1 N 22(TYR) 1 1 1 2.821 92.335 5 N 24(LEU) 1 O 20(GLN) 1 1 1 2.828 148.103 5 N 24(LEU) 1 O 21(THR) 1 1 1 2.749 110.592 5 N 24(LEU) 1 N 23(GLU) 1 1 1 2.805 95.990 5 N 25(GLU) 1 O 21(THR) 1 1 1 2.441 155.437 5 N 26(ARG) 1 O 22(TYR) 1 1 1 2.512 152.721 5 N 26(ARG) 1 N 25(GLU) 1 1 1 2.821 97.902 5 N 27(ARG) 1 O 23(GLU) 1 1 1 2.775 163.629 5 N 28(PHE) 1 O 24(LEU) 1 1 1 2.797 167.788 5 N 28(PHE) 1 N 27(ARG) 1 1 1 2.770 91.851 5 N 29(ARG) 1 O 25(GLU) 1 1 1 2.391 146.872 5 N 29(ARG) 1 O 26(ARG) 1 1 1 2.994 116.202 5 N 29(ARG) 1 N 28(PHE) 1 1 1 2.861 99.539 5 N 30(GLN) 1 O 26(ARG) 1 1 1 2.999 125.695 5 N 30(GLN) 1 N 29(ARG) 1 1 1 2.619 104.085 5 N 31(GLN) 1 O 27(ARG) 1 1 1 3.021 131.630 5 N 31(GLN) 1 O 28(PHE) 1 1 1 2.864 117.007 5 N 31(GLN) 1 N 30(GLN) 1 1 1 2.681 102.160 5 N 33(TYR) 1 N 32(ARG) 1 1 1 2.753 101.455 5 N 38(GLU) 1 O 35(SER) 1 1 1 3.189 126.019 5 N 40(GLU) 1 O 36(ALA) 1 1 1 2.484 164.817 5 N 40(GLU) 1 N 39(ARG) 1 1 1 2.827 96.976 5 N 41(HIS) 1 O 38(GLU) 1 1 1 2.878 118.686 5 N 41(HIS) 1 N 40(GLU) 1 1 1 2.698 98.385 5 N 42(LEU) 1 N 41(HIS) 1 1 1 2.744 94.000 5 N 43(ALA) 1 O 39(ARG) 1 1 1 2.748 149.145 5 N 43(ALA) 1 O 40(GLU) 1 1 1 2.679 100.943 5 N 43(ALA) 1 N 42(LEU) 1 1 1 2.746 99.851 5 N 44(SER) 1 O 40(GLU) 1 1 1 2.298 130.074 5 N 44(SER) 1 N 43(ALA) 1 1 1 2.679 96.429 5 N 45(LEU) 1 O 41(HIS) 1 1 1 2.812 119.423 5 N 45(LEU) 1 O 42(LEU) 1 1 1 3.105 132.730 5 N 45(LEU) 1 N 44(SER) 1 1 1 2.836 98.944 5 N 46(ILE) 1 O 42(LEU) 1 1 1 3.123 168.540 5 N 46(ILE) 1 N 45(LEU) 1 1 1 2.701 101.189 5 N 47(ARG) 1 O 43(ALA) 1 1 1 2.913 120.378 5 N 47(ARG) 1 N 46(ILE) 1 1 1 2.554 99.930 5 N 48(LEU) 1 O 43(ALA) 1 1 1 2.764 123.570 5 N 48(LEU) 1 N 47(ARG) 1 1 1 2.641 103.113 5 N 52(GLN) 1 O 49(THR) 1 1 1 2.296 120.858 5 N 52(GLN) 1 N 51(THR) 1 1 1 2.875 94.300 5 N 53(VAL) 1 O 49(THR) 1 1 1 3.238 135.958 5 N 53(VAL) 1 O 50(PRO) 1 1 1 3.045 118.584 5 N 54(LYS) 1 O 50(PRO) 1 1 1 2.698 169.342 5 N 55(ILE) 1 O 51(THR) 1 1 1 2.652 160.437 5 N 56(TRP) 1 O 53(VAL) 1 1 1 2.766 107.077 5 N 57(PHE) 1 O 53(VAL) 1 1 1 2.795 159.206 5 N 57(PHE) 1 N 56(TRP) 1 1 1 2.779 91.354 5 N 58(GLN) 1 O 54(LYS) 1 1 1 2.427 151.066 5 N 59(ASN) 1 O 55(ILE) 1 1 1 2.818 172.852 5 ND2 59(ASN) 1 N7 8(A ) 2 1 1 3.078 139.489 5 N 60(HIS) 1 N 59(ASN) 1 1 1 2.829 94.008 5 N 61(ARG) 1 O 58(GLN) 1 1 1 3.102 113.237 5 NE 61(ARG) 1 O 32(ARG) 1 1 1 2.562 117.540 5 N 63(LYS) 1 N 62(TYR) 1 1 1 2.849 96.042 5 N 64(THR) 1 O 60(HIS) 1 1 1 2.988 134.011 5 N 64(THR) 1 N 63(LYS) 1 1 1 2.765 102.302 5 N 65(LYS) 1 N 64(THR) 1 1 1 2.771 100.639 5 N 66(ARG) 1 N 65(LYS) 1 1 1 2.715 95.575 5 N 67(ALA) 1 O 64(THR) 1 1 1 2.820 115.067 5 N 67(ALA) 1 N 66(ARG) 1 1 1 2.827 97.123 5 N 68(GLN) 1 O 65(LYS) 1 1 1 2.906 117.693 5 N 68(GLN) 1 N 67(ALA) 1 1 1 2.679 102.016 5 N 69(ASN) 1 O 65(LYS) 1 1 1 3.003 129.975 5 N 69(ASN) 1 N 68(GLN) 1 1 1 2.665 100.727 5 N 70(GLU) 1 N 69(ASN) 1 1 1 2.697 101.025 5 N 71(LYS) 1 N 70(GLU) 1 1 1 2.711 100.596 5 N1 2(G ) 2 N3 15(C ) 3 1 1 2.765 118.543 5 N3 3(T ) 2 N1 14(A ) 3 1 1 2.628 168.500 5 N1 4(G ) 2 N3 13(C ) 3 1 1 2.456 146.318 5 N3 5(T ) 2 N1 12(A ) 3 1 1 3.110 151.911 5 N4 6(C ) 2 O6 11(G ) 3 1 1 2.886 163.202 5 N4 6(C ) 2 N1 11(G ) 3 1 1 3.148 113.665 5 N6 8(A ) 2 O4 9(T ) 3 1 1 2.800 155.801 5 N1 9(G ) 2 N3 8(C ) 3 1 1 2.918 141.540 5 N3 10(T ) 2 N1 7(A ) 3 1 1 2.767 164.549 5 N1 11(G ) 2 N3 6(C ) 3 1 1 3.046 138.630 5 N1 11(G ) 2 N4 6(C ) 3 1 1 3.067 149.699 5 N1 12(G ) 2 N3 5(C ) 3 1 1 3.143 143.110 5 N1 12(G ) 2 N4 5(C ) 3 1 1 3.083 123.966 5 N3 14(T ) 2 N1 3(A ) 3 1 1 2.770 163.883 5 N1 4(G ) 3 N3 13(C ) 2 1 1 3.218 125.122 5 N1 4(G ) 3 N4 13(C ) 2 1 1 3.009 128.364 5 N4 5(C ) 3 O6 12(G ) 2 1 1 2.701 102.396 5 N4 6(C ) 3 O6 11(G ) 2 1 1 3.116 123.222 5 N4 8(C ) 3 O6 9(G ) 2 1 1 2.404 146.825 5 N3 9(T ) 3 N1 8(A ) 2 1 1 2.507 168.812 5 N3 10(T ) 3 N1 7(A ) 2 1 1 3.104 142.860 5 N1 11(G ) 3 N3 6(C ) 2 1 1 2.786 145.176 5 N1 11(G ) 3 N4 6(C ) 2 1 1 3.148 137.049 5 N2 11(G ) 3 O2 6(C ) 2 1 1 3.088 116.191 5 N2 11(G ) 3 N3 7(A ) 2 1 1 2.805 98.255 5 N4 13(C ) 3 O6 4(G ) 2 1 1 3.062 155.307 5 N4 15(C ) 3 O6 2(G ) 2 1 1 2.798 134.217 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, 1nk2_wc.csv] Trying to match bases to eachother for number of bases: 32 Considering number of hydrogen bonds: 105 Results contains number of sets of co-planar bases: 7 Results: Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 15( C) Mol: 3 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 3 Model: 1 Entry: 1 Residue: 6( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( G) Mol: 3 Model: 1 Entry: 1 Residue: 8( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( T) Mol: 3 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 3 Model: 1 Entry: 1 Residue: 11( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 3 Model: 1 Entry: 1 Residue: 12( G) Mol: 2 Model: 1 Entry: 1 Residue: 5( C) Mol: 3 Model: 1 Entry: 1 Writing results to file: 1nk2_wc.csv Wattos started at: April 20, 2007 11:51:55 AM CDT Wattos stopped at: April 20, 2007 11:52:07 AM CDT Wattos took (#ms): 11371