Read libraries from system resource. Wattos started at: April 20, 2007 11:54:44 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/pdb1zq3.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 39200 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2306 Found number of new bond candidates: 2033 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: 67 Found number of new hydrogen bonds: 67 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 14(ILE) 1 O 10(THR) 1 1 1 3.091 170.390 5 N 15(ALA) 1 O 11(SER) 1 1 1 2.744 121.273 5 N 15(ALA) 1 N 14(ILE) 1 1 1 2.838 108.993 5 N 16(GLU) 1 O 12(SER) 1 1 1 3.055 169.805 5 N 17(LEU) 1 O 13(GLN) 1 1 1 2.827 167.564 5 N 18(GLU) 1 O 14(ILE) 1 1 1 3.144 160.559 5 N 19(GLN) 1 O 15(ALA) 1 1 1 3.216 143.929 5 N 20(HIS) 1 O 16(GLU) 1 1 1 2.847 162.135 5 N 21(PHE) 1 O 17(LEU) 1 1 1 2.988 149.712 5 N 22(LEU) 1 O 18(GLU) 1 1 1 3.105 156.917 5 N 23(GLN) 1 O 20(HIS) 1 1 1 3.106 140.347 5 N 23(GLN) 1 N 22(LEU) 1 1 1 2.809 101.085 5 N 24(GLY) 1 O 21(PHE) 1 1 1 2.857 143.509 5 N 24(GLY) 1 N 23(GLN) 1 1 1 2.835 102.654 5 N 26(TYR) 1 N 25(ARG) 1 1 1 2.779 108.962 5 N 32(LEU) 1 O 28(THR) 1 1 1 2.964 173.121 5 N 33(ALA) 1 O 29(ALA) 1 1 1 2.673 164.209 5 N 34(ASP) 1 O 30(PRO) 1 1 1 3.165 161.219 5 N 35(LEU) 1 O 31(ARG) 1 1 1 3.070 171.376 5 N 36(SER) 1 O 32(LEU) 1 1 1 3.029 156.087 5 N 37(ALA) 1 O 33(ALA) 1 1 1 3.113 167.208 5 N 39(LEU) 1 O 35(LEU) 1 1 1 2.843 165.461 5 N 40(ALA) 1 N 39(LEU) 1 1 1 2.664 102.278 5 N 44(ALA) 1 N 43(THR) 1 1 1 2.824 101.634 5 N 48(ILE) 1 O 44(ALA) 1 1 1 3.166 167.454 5 N 49(TRP) 1 O 45(GLN) 1 1 1 2.825 155.471 5 N 51(LYS) 1 O 47(LYS) 1 1 1 3.085 167.363 5 N 52(ASN) 1 O 48(ILE) 1 1 1 3.109 163.396 5 N 53(ARG) 1 O 49(TRP) 1 1 1 2.743 150.458 5 N 54(ARG) 1 O 50(PHE) 1 1 1 3.094 165.318 5 N 56(ARG) 1 O 52(ASN) 1 1 1 3.001 147.764 5 N 58(LYS) 1 O 54(ARG) 1 1 1 2.893 175.581 5 N 59(ILE) 1 O 55(ARG) 1 1 1 2.808 162.289 5 N 60(GLN) 1 O 56(ARG) 1 1 1 3.196 167.045 5 N1 1(G ) 2 N3 13(C ) 3 1 1 2.988 167.123 5 N2 1(G ) 2 O2 13(C ) 3 1 1 2.836 168.886 5 N3 3(T ) 2 N1 11(A ) 3 1 1 2.892 161.273 5 N4 4(C ) 2 O6 10(G ) 3 1 1 2.807 148.912 5 N3 5(T ) 2 N1 9(A ) 3 1 1 3.042 165.156 5 N6 6(A ) 2 O4 8(T ) 3 1 1 2.917 174.645 5 N6 7(A ) 2 O4 7(T ) 3 1 1 2.775 141.798 5 N3 8(T ) 2 N1 6(A ) 3 1 1 2.933 160.771 5 N4 9(C ) 2 O6 5(G ) 3 1 1 3.112 167.291 5 N4 10(C ) 2 O6 4(G ) 3 1 1 2.946 174.667 5 N4 11(C ) 2 O6 3(G ) 3 1 1 2.770 158.027 5 N4 12(C ) 2 O6 2(G ) 3 1 1 2.872 153.949 5 N1 13(G ) 2 N3 1(C ) 3 1 1 2.901 161.326 5 N2 13(G ) 2 O2 1(C ) 3 1 1 2.911 169.258 5 N4 1(C ) 3 O6 13(G ) 2 1 1 2.802 164.617 5 N1 2(G ) 3 N3 12(C ) 2 1 1 2.990 165.749 5 N2 2(G ) 3 O2 12(C ) 2 1 1 2.908 162.484 5 N1 3(G ) 3 N3 11(C ) 2 1 1 2.924 170.210 5 N2 3(G ) 3 O2 11(C ) 2 1 1 2.920 174.655 5 N1 4(G ) 3 N3 10(C ) 2 1 1 2.843 164.575 5 N2 4(G ) 3 O2 10(C ) 2 1 1 2.775 146.646 5 N1 5(G ) 3 N3 9(C ) 2 1 1 3.124 166.056 5 N2 5(G ) 3 O2 9(C ) 2 1 1 2.980 175.501 5 N6 6(A ) 3 O4 8(T ) 2 1 1 2.903 151.318 5 N3 7(T ) 3 N1 7(A ) 2 1 1 2.849 168.086 5 N3 8(T ) 3 N1 6(A ) 2 1 1 3.110 166.544 5 N6 9(A ) 3 O4 5(T ) 2 1 1 2.937 173.251 5 N1 10(G ) 3 N3 4(C ) 2 1 1 2.883 170.404 5 N2 10(G ) 3 O2 4(C ) 2 1 1 2.870 156.423 5 N6 11(A ) 3 O4 3(T ) 2 1 1 2.980 173.763 5 N1 12(G ) 3 N3 2(C ) 2 1 1 2.997 155.994 5 N2 12(G ) 3 O2 2(C ) 2 1 1 2.905 165.036 5 N4 13(C ) 3 O6 1(G ) 2 1 1 2.961 140.910 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, 1zq3_wc.csv] Trying to match bases to eachother for number of bases: 26 Considering number of hydrogen bonds: 67 Results contains number of sets of co-planar bases: 13 Results: Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 3 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 3 Model: 1 Entry: 1 Residue: 3( T) Mol: 2 Model: 1 Entry: 1 Residue: 11( A) Mol: 3 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 3 Model: 1 Entry: 1 Residue: 5( T) Mol: 2 Model: 1 Entry: 1 Residue: 9( A) Mol: 3 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 8( T) Mol: 3 Model: 1 Entry: 1 Residue: 7( A) Mol: 2 Model: 1 Entry: 1 Residue: 7( T) Mol: 3 Model: 1 Entry: 1 Residue: 8( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 3 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 5( G) Mol: 3 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( G) Mol: 3 Model: 1 Entry: 1 Residue: 11( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 3 Model: 1 Entry: 1 Residue: 12( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 3 Model: 1 Entry: 1 Residue: 13( G) Mol: 2 Model: 1 Entry: 1 Residue: 1( C) Mol: 3 Model: 1 Entry: 1 Writing results to file: 1zq3_wc.csv Wattos started at: April 20, 2007 11:54:44 AM CDT Wattos stopped at: April 20, 2007 11:54:54 AM CDT Wattos took (#ms): 10149