Read libraries from system resource. Wattos started at: April 20, 2007 11:53:18 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/pdb1qry.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 27740 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1596 Found number of new bond candidates: 1403 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: 36 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 25(TYR) 1 O 21(LYS) 1 1 1 124.968 5 N 25(TYR) 1 O 22(ALA) 1 1 1 117.525 5 N 25(TYR) 1 N 24(THR) 1 1 1 97.917 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 28(GLU) 1 O 24(THR) 1 1 1 112.438 5 N 28(GLU) 1 O 25(TYR) 1 1 1 130.785 5 N 28(GLU) 1 N 27(LEU) 1 1 1 101.483 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 57(LYS) 1 O 53(PRO) 1 1 1 148.970 5 N 57(LYS) 1 O 54(THR) 1 1 1 106.614 5 N 57(LYS) 1 N 56(VAL) 1 1 1 93.840 5 Found number of new hydrogen bonds: 36 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 22(ALA) 1 N 21(LYS) 1 1 1 2.563 107.375 5 N 23(GLN) 1 O 20(THR) 1 1 1 2.703 95.348 5 N 25(TYR) 1 O 21(LYS) 1 1 1 3.080 124.968 5 N 25(TYR) 1 O 22(ALA) 1 1 1 2.561 117.525 5 N 25(TYR) 1 N 24(THR) 1 1 1 2.777 97.917 5 N 26(GLU) 1 O 22(ALA) 1 1 1 2.960 135.876 5 N 27(LEU) 1 O 23(GLN) 1 1 1 2.615 141.958 5 N 28(GLU) 1 O 24(THR) 1 1 1 2.543 112.438 5 N 28(GLU) 1 O 25(TYR) 1 1 1 2.424 130.785 5 N 28(GLU) 1 N 27(LEU) 1 1 1 2.698 101.483 5 N 29(ARG) 1 O 25(TYR) 1 1 1 2.662 146.797 5 N 29(ARG) 1 N 28(GLU) 1 1 1 2.671 101.690 5 N 30(ARG) 1 O 26(GLU) 1 1 1 2.858 157.137 5 N 30(ARG) 1 N 29(ARG) 1 1 1 2.777 97.853 5 N 31(PHE) 1 N 30(ARG) 1 1 1 2.804 96.639 5 N 34(GLN) 1 O 30(ARG) 1 1 1 2.738 123.939 5 N 34(GLN) 1 N 33(GLN) 1 1 1 2.636 107.240 5 N 36(TYR) 1 N 35(ARG) 1 1 1 2.583 107.607 5 N 41(GLU) 1 N 40(PRO) 1 1 1 2.748 103.104 5 N 42(ARG) 1 N 41(GLU) 1 1 1 2.750 96.797 5 N 46(THR) 1 O 42(ARG) 1 1 1 3.296 149.820 5 N 48(LEU) 1 O 45(LEU) 1 1 1 2.155 114.297 5 N 50(ARG) 1 N 49(ILE) 1 1 1 2.738 103.912 5 N 56(VAL) 1 O 52(THR) 1 1 1 2.759 146.407 5 N 57(LYS) 1 O 53(PRO) 1 1 1 3.218 148.970 5 N 57(LYS) 1 O 54(THR) 1 1 1 2.563 106.614 5 N 57(LYS) 1 N 56(VAL) 1 1 1 2.835 93.840 5 N 58(ILE) 1 O 54(THR) 1 1 1 2.752 167.956 5 N 59(TRP) 1 O 55(GLN) 1 1 1 2.967 140.748 5 N 59(TRP) 1 N 58(ILE) 1 1 1 2.729 100.684 5 N 66(LYS) 1 O 63(HIS) 1 1 1 2.549 100.921 5 N 66(LYS) 1 N 65(TYR) 1 1 1 2.841 96.567 5 N 67(THR) 1 O 63(HIS) 1 1 1 2.274 155.757 5 N 67(THR) 1 N 66(LYS) 1 1 1 2.828 96.491 5 N 68(LYS) 1 N 67(THR) 1 1 1 2.618 106.377 5 N 73(GLU) 1 N 72(ASN) 1 1 1 2.733 101.355 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, 1qry_wc.csv] Trying to match bases to eachother for number of bases: 0 Considering number of hydrogen bonds: 36 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: 1qry_wc.csv Wattos started at: April 20, 2007 11:53:18 AM CDT Wattos stopped at: April 20, 2007 11:53:21 AM CDT Wattos took (#ms): 3096