Starting phenix.real_space_refine on Mon Sep 14 17:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0h_0567/09_2026/6o0h_0567.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 8 5.49 5 S 192 5.16 5 Cl 4 4.86 5 C 20480 2.51 5 N 5400 2.21 5 O 5920 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32012 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "B" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "C" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "D" Number of atoms: 7946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1023, 7938 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 2 bond proxies already assigned to first conformer: 8100 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'ADP': 1, 'LBG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.68, per 1000 atoms: 0.36 Number of scatterers: 32012 At special positions: 0 Unit cell: (147.41, 160.136, 174.983, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 192 16.00 P 8 15.00 F 8 9.00 O 5920 8.00 N 5400 7.00 C 20480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 2.3 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 40 sheets defined 45.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.706A pdb=" N LYS A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.786A pdb=" N LEU A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.630A pdb=" N CYS A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.543A pdb=" N LEU A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.762A pdb=" N CYS A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.973A pdb=" N PHE A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.686A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.530A pdb=" N LEU A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.888A pdb=" N GLY A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 562 removed outlier: 4.097A pdb=" N ALA A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.660A pdb=" N ARG A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 696 through 706 removed outlier: 4.050A pdb=" N HIS A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 733 removed outlier: 3.795A pdb=" N CYS A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 750 removed outlier: 3.524A pdb=" N ALA A 749 " --> pdb=" O GLY A 746 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 750 " --> pdb=" O THR A 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 746 through 750' Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 806 removed outlier: 3.705A pdb=" N ASP A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 878 removed outlier: 4.064A pdb=" N GLY A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 897 removed outlier: 3.735A pdb=" N PHE A 889 " --> pdb=" O TYR A 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 891 " --> pdb=" O CYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 removed outlier: 4.013A pdb=" N CYS A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 removed outlier: 3.844A pdb=" N SER A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 removed outlier: 3.582A pdb=" N LYS A 944 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 966 removed outlier: 3.638A pdb=" N PHE A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 998 removed outlier: 3.602A pdb=" N GLN A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 3.512A pdb=" N ALA A1007 " --> pdb=" O LEU A1003 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 4.166A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1034 " --> pdb=" O GLY A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1049 through 1055 removed outlier: 3.739A pdb=" N GLY A1055 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1079 removed outlier: 3.752A pdb=" N VAL A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1063 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 39 through 47 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.706A pdb=" N LYS B 68 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.786A pdb=" N LEU B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.631A pdb=" N CYS B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.526A pdb=" N LEU B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.732A pdb=" N CYS B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.568A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.978A pdb=" N PHE B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.693A pdb=" N LYS B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.537A pdb=" N LEU B 388 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 removed outlier: 3.899A pdb=" N GLY B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 555 through 562 removed outlier: 4.075A pdb=" N ALA B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 Processing helix chain 'B' and resid 602 through 617 removed outlier: 3.640A pdb=" N ARG B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.035A pdb=" N HIS B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 733 removed outlier: 3.741A pdb=" N CYS B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.541A pdb=" N ALA B 749 " --> pdb=" O GLY B 746 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B 750 " --> pdb=" O THR B 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 746 through 750' Processing helix chain 'B' and resid 767 through 770 Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 806 removed outlier: 3.617A pdb=" N ASP B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 829 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 878 removed outlier: 4.063A pdb=" N GLY B 874 " --> pdb=" O GLY B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.735A pdb=" N PHE B 889 " --> pdb=" O TYR B 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 891 " --> pdb=" O CYS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 916 removed outlier: 4.004A pdb=" N CYS B 913 " --> pdb=" O ASN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 929 removed outlier: 3.840A pdb=" N SER B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 927 " --> pdb=" O SER B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 removed outlier: 3.582A pdb=" N LYS B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 952 " --> pdb=" O LYS B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 966 removed outlier: 3.640A pdb=" N PHE B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 998 removed outlier: 3.597A pdb=" N GLN B 988 " --> pdb=" O ASP B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1016 removed outlier: 3.511A pdb=" N ALA B1007 " --> pdb=" O LEU B1003 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B1009 " --> pdb=" O ASP B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 4.164A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B1034 " --> pdb=" O GLY B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1049 through 1055 removed outlier: 3.739A pdb=" N GLY B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1079 removed outlier: 3.747A pdb=" N VAL B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1063 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.706A pdb=" N LYS C 68 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.787A pdb=" N LEU C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.631A pdb=" N CYS C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.524A pdb=" N LEU C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 removed outlier: 3.729A pdb=" N CYS C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.565A pdb=" N THR C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 363 removed outlier: 3.978A pdb=" N PHE C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 358 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.695A pdb=" N LYS C 369 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.537A pdb=" N LEU C 388 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 419 removed outlier: 3.899A pdb=" N GLY C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 555 through 562 removed outlier: 4.080A pdb=" N ALA C 559 " --> pdb=" O ASN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 Processing helix chain 'C' and resid 602 through 617 removed outlier: 3.640A pdb=" N ARG C 607 " --> pdb=" O GLU C 603 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 666 through 676 Processing helix chain 'C' and resid 696 through 706 removed outlier: 4.034A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 removed outlier: 3.742A pdb=" N CYS C 728 " --> pdb=" O GLU C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 750 removed outlier: 3.525A pdb=" N ALA C 749 " --> pdb=" O GLY C 746 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR C 750 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 750' Processing helix chain 'C' and resid 767 through 770 Processing helix chain 'C' and resid 771 through 781 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 806 removed outlier: 3.623A pdb=" N ASP C 803 " --> pdb=" O SER C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 829 Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 878 removed outlier: 4.062A pdb=" N GLY C 874 " --> pdb=" O GLY C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 897 removed outlier: 3.734A pdb=" N PHE C 889 " --> pdb=" O TYR C 885 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 891 " --> pdb=" O CYS C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 916 removed outlier: 3.995A pdb=" N CYS C 913 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 929 removed outlier: 3.846A pdb=" N SER C 926 " --> pdb=" O SER C 922 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 927 " --> pdb=" O SER C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 952 removed outlier: 3.554A pdb=" N LYS C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 951 " --> pdb=" O SER C 947 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 952 " --> pdb=" O LYS C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 966 removed outlier: 3.640A pdb=" N PHE C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 998 removed outlier: 3.599A pdb=" N GLN C 988 " --> pdb=" O ASP C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1016 removed outlier: 3.510A pdb=" N ALA C1007 " --> pdb=" O LEU C1003 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C1009 " --> pdb=" O ASP C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 4.162A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C1034 " --> pdb=" O GLY C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1049 Processing helix chain 'C' and resid 1049 through 1055 removed outlier: 3.740A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1079 removed outlier: 3.757A pdb=" N VAL C1062 " --> pdb=" O ASN C1058 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C1063 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.706A pdb=" N LYS D 68 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 177 through 195 removed outlier: 3.787A pdb=" N LEU D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.631A pdb=" N CYS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 removed outlier: 3.516A pdb=" N LEU D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 removed outlier: 3.750A pdb=" N CYS D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 349 through 363 removed outlier: 3.975A pdb=" N PHE D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 358 " --> pdb=" O PHE D 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.981A pdb=" N LYS D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.543A pdb=" N LEU D 388 " --> pdb=" O TYR D 384 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 419 removed outlier: 3.905A pdb=" N GLY D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 562 removed outlier: 4.096A pdb=" N ALA D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 602 through 617 removed outlier: 3.646A pdb=" N ARG D 607 " --> pdb=" O GLU D 603 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 696 through 706 removed outlier: 4.040A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 removed outlier: 3.778A pdb=" N CYS D 728 " --> pdb=" O GLU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 750 removed outlier: 3.523A pdb=" N ALA D 749 " --> pdb=" O GLY D 746 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR D 750 " --> pdb=" O THR D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 750' Processing helix chain 'D' and resid 767 through 770 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 806 removed outlier: 3.625A pdb=" N ASP D 803 " --> pdb=" O SER D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 829 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 878 removed outlier: 4.061A pdb=" N GLY D 874 " --> pdb=" O GLY D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.725A pdb=" N PHE D 889 " --> pdb=" O TYR D 885 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 891 " --> pdb=" O CYS D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 removed outlier: 3.995A pdb=" N CYS D 913 " --> pdb=" O ASN D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 929 removed outlier: 3.850A pdb=" N SER D 926 " --> pdb=" O SER D 922 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 952 removed outlier: 3.580A pdb=" N LYS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 951 " --> pdb=" O SER D 947 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 952 " --> pdb=" O LYS D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.641A pdb=" N PHE D 959 " --> pdb=" O ILE D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 998 removed outlier: 3.599A pdb=" N GLN D 988 " --> pdb=" O ASP D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1016 removed outlier: 3.511A pdb=" N ALA D1007 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D1009 " --> pdb=" O ASP D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.161A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D1034 " --> pdb=" O GLY D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1049 Processing helix chain 'D' and resid 1049 through 1055 removed outlier: 3.733A pdb=" N GLY D1055 " --> pdb=" O TYR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1079 removed outlier: 3.751A pdb=" N VAL D1062 " --> pdb=" O ASN D1058 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D1063 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 218 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 200 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 220 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR A 199 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA A 125 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU A 201 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE A 123 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A 203 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 121 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 124 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 218 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 200 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS A 220 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 206 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.825A pdb=" N VAL A 57 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL A 74 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA A 93 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 100 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 278 removed outlier: 7.133A pdb=" N ILE A 375 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE A 405 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 377 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 6.565A pdb=" N VAL A 501 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 500 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 630 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 686 removed outlier: 7.087A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A 716 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 660 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLU A 718 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N TRP A 743 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 715 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE A 745 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 717 " --> pdb=" O ILE A 745 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 823 through 824 removed outlier: 6.440A pdb=" N MET A 823 " --> pdb=" O ARG B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AB3, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.349A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR B 199 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA B 125 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 201 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 123 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN B 203 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL B 121 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 124 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.349A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 206 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.825A pdb=" N VAL B 57 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 74 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA B 93 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 100 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.551A pdb=" N THR B 267 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 275 through 278 removed outlier: 7.158A pdb=" N ILE B 375 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE B 405 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 377 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 537 through 543 removed outlier: 6.555A pdb=" N VAL B 501 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 500 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 629 through 630 Processing sheet with id=AC2, first strand: chain 'B' and resid 681 through 686 removed outlier: 7.070A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU B 718 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 713 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N TRP B 743 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 715 " --> pdb=" O TRP B 743 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE B 745 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY B 717 " --> pdb=" O ILE B 745 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA C 219 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 218 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 200 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS C 220 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR C 199 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA C 125 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU C 201 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 123 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN C 203 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL C 121 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR C 124 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA C 219 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 218 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 200 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS C 220 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 206 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.825A pdb=" N VAL C 57 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 74 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA C 93 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 100 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.560A pdb=" N THR C 267 " --> pdb=" O TYR C 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 275 through 278 removed outlier: 7.156A pdb=" N ILE C 375 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE C 405 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 377 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 537 through 543 removed outlier: 6.541A pdb=" N VAL C 501 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 500 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AD2, first strand: chain 'C' and resid 681 through 686 removed outlier: 7.070A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU C 718 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TRP C 743 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 715 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 745 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY C 717 " --> pdb=" O ILE C 745 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.451A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 834 through 835 Processing sheet with id=AD5, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 124 " --> pdb=" O TYR D 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.350A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 206 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.825A pdb=" N VAL D 57 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL D 74 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.502A pdb=" N ALA D 93 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 100 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 267 through 268 removed outlier: 3.550A pdb=" N THR D 267 " --> pdb=" O TYR D 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 275 through 278 removed outlier: 7.146A pdb=" N ILE D 375 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE D 405 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 377 " --> pdb=" O PHE D 405 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 537 through 543 removed outlier: 6.549A pdb=" N VAL D 501 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 500 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 629 through 630 Processing sheet with id=AE4, first strand: chain 'D' and resid 681 through 686 removed outlier: 7.073A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLU D 718 " --> pdb=" O VAL D 660 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 745 " --> pdb=" O VAL D 715 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY D 717 " --> pdb=" O ILE D 745 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 1257 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9637 1.33 - 1.45: 5378 1.45 - 1.57: 17373 1.57 - 1.69: 12 1.69 - 1.81: 324 Bond restraints: 32724 Sorted by residual: bond pdb=" C ARG C 244 " pdb=" N GLU C 245 " ideal model delta sigma weight residual 1.330 1.243 0.087 1.32e-02 5.74e+03 4.37e+01 bond pdb=" C ARG B 244 " pdb=" N GLU B 245 " ideal model delta sigma weight residual 1.330 1.247 0.083 1.32e-02 5.74e+03 3.97e+01 bond pdb=" CA TYR B 542 " pdb=" CB TYR B 542 " ideal model delta sigma weight residual 1.528 1.486 0.043 1.51e-02 4.39e+03 8.00e+00 bond pdb=" CB THR C 925 " pdb=" CG2 THR C 925 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.95e+00 bond pdb=" CA TYR D 542 " pdb=" CB TYR D 542 " ideal model delta sigma weight residual 1.528 1.486 0.042 1.51e-02 4.39e+03 7.91e+00 ... (remaining 32719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 43068 2.98 - 5.96: 1145 5.96 - 8.94: 80 8.94 - 11.92: 27 11.92 - 14.90: 8 Bond angle restraints: 44328 Sorted by residual: angle pdb=" N TRP C 877 " pdb=" CA TRP C 877 " pdb=" C TRP C 877 " ideal model delta sigma weight residual 111.14 118.27 -7.13 1.08e+00 8.57e-01 4.35e+01 angle pdb=" N TRP D 877 " pdb=" CA TRP D 877 " pdb=" C TRP D 877 " ideal model delta sigma weight residual 111.14 118.24 -7.10 1.08e+00 8.57e-01 4.32e+01 angle pdb=" N TRP A 877 " pdb=" CA TRP A 877 " pdb=" C TRP A 877 " ideal model delta sigma weight residual 111.14 118.19 -7.05 1.08e+00 8.57e-01 4.26e+01 angle pdb=" N TRP B 877 " pdb=" CA TRP B 877 " pdb=" C TRP B 877 " ideal model delta sigma weight residual 111.14 118.17 -7.03 1.08e+00 8.57e-01 4.24e+01 angle pdb=" N ARG A 829 " pdb=" CA ARG A 829 " pdb=" C ARG A 829 " ideal model delta sigma weight residual 113.12 106.60 6.52 1.25e+00 6.40e-01 2.72e+01 ... (remaining 44323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 19317 34.94 - 69.89: 153 69.89 - 104.83: 16 104.83 - 139.77: 4 139.77 - 174.71: 2 Dihedral angle restraints: 19492 sinusoidal: 7828 harmonic: 11664 Sorted by residual: dihedral pdb=" C5' ADP D2002 " pdb=" O5' ADP D2002 " pdb=" PA ADP D2002 " pdb=" O2A ADP D2002 " ideal model delta sinusoidal sigma weight residual 300.00 125.29 174.71 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C2002 " pdb=" O5' ADP C2002 " pdb=" PA ADP C2002 " pdb=" O2A ADP C2002 " ideal model delta sinusoidal sigma weight residual 300.00 125.33 174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C2002 " pdb=" O3A ADP C2002 " pdb=" PA ADP C2002 " pdb=" PB ADP C2002 " ideal model delta sinusoidal sigma weight residual -60.00 74.42 -134.42 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 19489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3676 0.065 - 0.130: 1034 0.130 - 0.195: 166 0.195 - 0.260: 34 0.260 - 0.325: 6 Chirality restraints: 4916 Sorted by residual: chirality pdb=" CB ILE A 911 " pdb=" CA ILE A 911 " pdb=" CG1 ILE A 911 " pdb=" CG2 ILE A 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE D 911 " pdb=" CA ILE D 911 " pdb=" CG1 ILE D 911 " pdb=" CG2 ILE D 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE C 911 " pdb=" CA ILE C 911 " pdb=" CG1 ILE C 911 " pdb=" CG2 ILE C 911 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4913 not shown) Planarity restraints: 5656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 901 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO A 902 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 901 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO C 902 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 902 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 902 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 901 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO B 902 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 902 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 902 " 0.041 5.00e-02 4.00e+02 ... (remaining 5653 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8037 2.79 - 3.32: 28147 3.32 - 3.84: 52527 3.84 - 4.37: 60570 4.37 - 4.90: 104236 Nonbonded interactions: 253517 Sorted by model distance: nonbonded pdb=" O GLU C1011 " pdb=" OG1 THR C1015 " model vdw 2.262 3.040 nonbonded pdb=" O GLU B1011 " pdb=" OG1 THR B1015 " model vdw 2.262 3.040 nonbonded pdb=" O GLU A1011 " pdb=" OG1 THR A1015 " model vdw 2.263 3.040 nonbonded pdb=" O THR A 35 " pdb=" OG1 THR A 38 " model vdw 2.263 3.040 nonbonded pdb=" O THR B 35 " pdb=" OG1 THR B 38 " model vdw 2.263 3.040 ... (remaining 253512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.700 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 32724 Z= 0.387 Angle : 1.165 14.896 44328 Z= 0.660 Chirality : 0.063 0.325 4916 Planarity : 0.009 0.076 5656 Dihedral : 10.651 174.713 12084 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.35 % Allowed : 2.47 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.11), residues: 4076 helix: -3.26 (0.08), residues: 1736 sheet: -1.80 (0.21), residues: 564 loop : -2.29 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 915 TYR 0.033 0.004 TYR D 854 PHE 0.036 0.004 PHE D 863 TRP 0.045 0.005 TRP B 502 HIS 0.013 0.003 HIS D 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00885 / 0.39 (32724) covalent geometry : angle 1.16492 / 0.66 (44328) hydrogen bonds : bond 0.17440 / 11.62 ( 1241) hydrogen bonds : angle 7.64492 / 5.31 ( 3576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 954 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8062 (mt) cc_final: 0.7518 (pt) REVERT: A 265 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7742 (mtpp) REVERT: A 327 MET cc_start: 0.6963 (mmm) cc_final: 0.6732 (mmm) REVERT: A 412 THR cc_start: 0.8934 (p) cc_final: 0.8689 (p) REVERT: A 556 MET cc_start: 0.6595 (mtp) cc_final: 0.6362 (mtp) REVERT: A 618 VAL cc_start: 0.8822 (t) cc_final: 0.8496 (p) REVERT: B 202 ILE cc_start: 0.8134 (mt) cc_final: 0.7589 (pt) REVERT: B 265 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7736 (mtpp) REVERT: B 327 MET cc_start: 0.6894 (mmm) cc_final: 0.6674 (mmm) REVERT: B 412 THR cc_start: 0.8909 (p) cc_final: 0.8663 (p) REVERT: C 202 ILE cc_start: 0.8136 (mt) cc_final: 0.7598 (pt) REVERT: C 265 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7739 (mtpp) REVERT: C 327 MET cc_start: 0.6907 (mmm) cc_final: 0.6682 (mmm) REVERT: C 412 THR cc_start: 0.8902 (p) cc_final: 0.8663 (p) REVERT: D 202 ILE cc_start: 0.8085 (mt) cc_final: 0.7543 (pt) REVERT: D 265 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7757 (mtpp) REVERT: D 327 MET cc_start: 0.6963 (mmm) cc_final: 0.6689 (mmm) REVERT: D 412 THR cc_start: 0.8904 (p) cc_final: 0.8664 (p) REVERT: D 618 VAL cc_start: 0.8838 (t) cc_final: 0.8527 (p) outliers start: 12 outliers final: 8 residues processed: 966 average time/residue: 0.2186 time to fit residues: 330.3682 Evaluate side-chains 504 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 496 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 233 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0970 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 61 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 510 GLN A 590 GLN A1072 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 61 GLN B 172 HIS B 410 HIS B 510 GLN B 590 GLN B1072 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 61 GLN C 172 HIS C 410 HIS C 510 GLN C 590 GLN C1072 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 61 GLN D 172 HIS D 410 HIS D 510 GLN D 590 GLN D1072 HIS ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.168251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139548 restraints weight = 101914.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142580 restraints weight = 120404.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146169 restraints weight = 52079.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146009 restraints weight = 33864.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147585 restraints weight = 26931.230| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32724 Z= 0.141 Angle : 0.694 11.683 44328 Z= 0.351 Chirality : 0.048 0.209 4916 Planarity : 0.007 0.072 5656 Dihedral : 8.121 164.332 4516 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.21 % Allowed : 10.65 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.12), residues: 4076 helix: -1.77 (0.10), residues: 1768 sheet: -1.44 (0.22), residues: 552 loop : -1.65 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 65 TYR 0.022 0.002 TYR A 319 PHE 0.018 0.002 PHE A 110 TRP 0.016 0.001 TRP C 502 HIS 0.008 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (32724) covalent geometry : angle 0.69371 / 0.35 (44328) hydrogen bonds : bond 0.04212 / 2.81 ( 1241) hydrogen bonds : angle 5.09707 / 3.56 ( 3576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 623 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6700 (mtp-110) cc_final: 0.6123 (mtt90) REVERT: A 202 ILE cc_start: 0.8355 (mt) cc_final: 0.7842 (pt) REVERT: A 232 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7878 (mmmt) REVERT: A 233 TRP cc_start: 0.8546 (OUTLIER) cc_final: 0.7964 (m-10) REVERT: A 781 GLU cc_start: 0.7568 (tp30) cc_final: 0.6857 (mt-10) REVERT: A 955 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 1060 ILE cc_start: 0.8834 (tp) cc_final: 0.8462 (tp) REVERT: A 1075 ASP cc_start: 0.8613 (t70) cc_final: 0.8173 (t0) REVERT: B 65 ARG cc_start: 0.6765 (mtp-110) cc_final: 0.6263 (mtt90) REVERT: B 202 ILE cc_start: 0.8297 (mt) cc_final: 0.7789 (pt) REVERT: B 232 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (mmmt) REVERT: B 233 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: B 955 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (tp) REVERT: B 1060 ILE cc_start: 0.8874 (tp) cc_final: 0.8500 (tp) REVERT: B 1075 ASP cc_start: 0.8640 (t70) cc_final: 0.8174 (t0) REVERT: C 65 ARG cc_start: 0.6772 (mtp-110) cc_final: 0.6294 (mtt90) REVERT: C 202 ILE cc_start: 0.8290 (mt) cc_final: 0.7778 (pt) REVERT: C 232 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (mmmt) REVERT: C 233 TRP cc_start: 0.8655 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: C 1060 ILE cc_start: 0.8854 (tp) cc_final: 0.8502 (tp) REVERT: C 1075 ASP cc_start: 0.8637 (t70) cc_final: 0.8169 (t0) REVERT: D 65 ARG cc_start: 0.6763 (mtp-110) cc_final: 0.6271 (mtt90) REVERT: D 202 ILE cc_start: 0.8349 (mt) cc_final: 0.7852 (pt) REVERT: D 232 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7864 (mmmt) REVERT: D 233 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7941 (m-10) REVERT: D 955 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 1060 ILE cc_start: 0.8871 (tp) cc_final: 0.8504 (tp) REVERT: D 1075 ASP cc_start: 0.8620 (t70) cc_final: 0.8141 (t0) outliers start: 75 outliers final: 38 residues processed: 670 average time/residue: 0.2200 time to fit residues: 236.4474 Evaluate side-chains 505 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 456 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 230 optimal weight: 3.9990 chunk 370 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 239 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 381 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 908 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132348 restraints weight = 102106.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130362 restraints weight = 80177.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130397 restraints weight = 58573.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130900 restraints weight = 36712.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131363 restraints weight = 33948.586| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32724 Z= 0.190 Angle : 0.681 11.405 44328 Z= 0.343 Chirality : 0.048 0.205 4916 Planarity : 0.005 0.058 5656 Dihedral : 7.449 153.681 4516 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 13.62 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 4076 helix: -1.14 (0.11), residues: 1780 sheet: -0.97 (0.23), residues: 560 loop : -1.49 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 65 TYR 0.017 0.002 TYR A 319 PHE 0.020 0.002 PHE C 863 TRP 0.016 0.002 TRP D 84 HIS 0.005 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (32724) covalent geometry : angle 0.68062 / 0.34 (44328) hydrogen bonds : bond 0.04006 / 2.68 ( 1241) hydrogen bonds : angle 4.86615 / 3.41 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 458 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6807 (tt0) cc_final: 0.6571 (tt0) REVERT: A 65 ARG cc_start: 0.6962 (mtp-110) cc_final: 0.6172 (mtt90) REVERT: A 202 ILE cc_start: 0.8646 (mt) cc_final: 0.8069 (pt) REVERT: A 233 TRP cc_start: 0.8823 (OUTLIER) cc_final: 0.8502 (m-10) REVERT: A 586 MET cc_start: 0.8289 (mtp) cc_final: 0.8065 (mtt) REVERT: A 630 LYS cc_start: 0.8629 (tttt) cc_final: 0.8391 (tttt) REVERT: A 1060 ILE cc_start: 0.8970 (tp) cc_final: 0.8550 (tp) REVERT: B 13 GLU cc_start: 0.6849 (tt0) cc_final: 0.6598 (tt0) REVERT: B 65 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6187 (mtt90) REVERT: B 202 ILE cc_start: 0.8614 (mt) cc_final: 0.8016 (pt) REVERT: B 233 TRP cc_start: 0.8805 (OUTLIER) cc_final: 0.8436 (m-10) REVERT: B 586 MET cc_start: 0.8271 (mtp) cc_final: 0.8042 (mtt) REVERT: B 630 LYS cc_start: 0.8614 (tttt) cc_final: 0.8389 (tttt) REVERT: B 1060 ILE cc_start: 0.9008 (tp) cc_final: 0.8576 (tp) REVERT: C 13 GLU cc_start: 0.6853 (tt0) cc_final: 0.6596 (tt0) REVERT: C 65 ARG cc_start: 0.6919 (mtp-110) cc_final: 0.6204 (mtt90) REVERT: C 202 ILE cc_start: 0.8594 (mt) cc_final: 0.7997 (pt) REVERT: C 233 TRP cc_start: 0.8805 (OUTLIER) cc_final: 0.8432 (m-10) REVERT: C 630 LYS cc_start: 0.8614 (tttt) cc_final: 0.8392 (tttt) REVERT: C 1060 ILE cc_start: 0.8971 (tp) cc_final: 0.8542 (tp) REVERT: D 13 GLU cc_start: 0.6820 (tt0) cc_final: 0.6579 (tt0) REVERT: D 65 ARG cc_start: 0.6976 (mtp-110) cc_final: 0.6227 (mtt90) REVERT: D 202 ILE cc_start: 0.8638 (mt) cc_final: 0.8063 (pt) REVERT: D 233 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: D 327 MET cc_start: 0.6203 (mmm) cc_final: 0.5895 (mmm) REVERT: D 586 MET cc_start: 0.8261 (mtp) cc_final: 0.8042 (mtt) REVERT: D 630 LYS cc_start: 0.8623 (tttt) cc_final: 0.8378 (tttt) REVERT: D 1060 ILE cc_start: 0.8983 (tp) cc_final: 0.8576 (tp) outliers start: 77 outliers final: 45 residues processed: 501 average time/residue: 0.2103 time to fit residues: 172.1952 Evaluate side-chains 469 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 420 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1011 GLU Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 233 TRP Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1049 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 234 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135685 restraints weight = 91661.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137381 restraints weight = 88900.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140444 restraints weight = 52154.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141310 restraints weight = 31527.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142095 restraints weight = 28577.139| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32724 Z= 0.129 Angle : 0.619 10.294 44328 Z= 0.308 Chirality : 0.046 0.196 4916 Planarity : 0.005 0.059 5656 Dihedral : 6.603 142.739 4500 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.56 % Allowed : 14.62 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.13), residues: 4076 helix: -0.61 (0.12), residues: 1800 sheet: -0.72 (0.23), residues: 560 loop : -1.33 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 422 TYR 0.015 0.002 TYR D 319 PHE 0.017 0.001 PHE A 197 TRP 0.016 0.001 TRP D 84 HIS 0.018 0.001 HIS A 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (32724) covalent geometry : angle 0.61850 / 0.31 (44328) hydrogen bonds : bond 0.03463 / 2.32 ( 1241) hydrogen bonds : angle 4.52395 / 3.18 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 457 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6823 (mtp-110) cc_final: 0.6235 (mtt90) REVERT: A 202 ILE cc_start: 0.8561 (mt) cc_final: 0.8034 (pt) REVERT: A 292 ILE cc_start: 0.8441 (mm) cc_final: 0.8060 (mp) REVERT: A 364 TYR cc_start: 0.5725 (m-80) cc_final: 0.5047 (m-10) REVERT: A 586 MET cc_start: 0.8233 (mtp) cc_final: 0.8020 (mtt) REVERT: A 1060 ILE cc_start: 0.8924 (tp) cc_final: 0.8478 (tp) REVERT: B 65 ARG cc_start: 0.6830 (mtp-110) cc_final: 0.6266 (mtt90) REVERT: B 202 ILE cc_start: 0.8597 (mt) cc_final: 0.8067 (pt) REVERT: B 233 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.8384 (m-10) REVERT: B 292 ILE cc_start: 0.8436 (mm) cc_final: 0.8081 (mp) REVERT: B 1060 ILE cc_start: 0.8914 (tp) cc_final: 0.8481 (tp) REVERT: C 65 ARG cc_start: 0.6780 (mtp-110) cc_final: 0.6293 (mtt90) REVERT: C 202 ILE cc_start: 0.8562 (mt) cc_final: 0.8041 (pt) REVERT: C 233 TRP cc_start: 0.8781 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: C 292 ILE cc_start: 0.8433 (mm) cc_final: 0.8064 (mp) REVERT: C 1060 ILE cc_start: 0.8902 (tp) cc_final: 0.8454 (tp) REVERT: D 65 ARG cc_start: 0.6766 (mtp-110) cc_final: 0.6261 (mtt90) REVERT: D 202 ILE cc_start: 0.8540 (mt) cc_final: 0.8027 (pt) REVERT: D 512 MET cc_start: 0.8415 (mmm) cc_final: 0.7750 (mtt) REVERT: D 1057 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8470 (mt) REVERT: D 1060 ILE cc_start: 0.8920 (tp) cc_final: 0.8509 (tp) outliers start: 53 outliers final: 32 residues processed: 488 average time/residue: 0.1983 time to fit residues: 159.1249 Evaluate side-chains 426 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 391 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 823 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 823 MET Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 323 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 368 optimal weight: 9.9990 chunk 210 optimal weight: 0.0570 chunk 168 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129779 restraints weight = 78565.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132298 restraints weight = 111159.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135270 restraints weight = 58238.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137006 restraints weight = 33173.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137851 restraints weight = 25439.445| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 32724 Z= 0.213 Angle : 0.677 10.336 44328 Z= 0.339 Chirality : 0.048 0.197 4916 Planarity : 0.005 0.058 5656 Dihedral : 6.446 139.478 4496 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.91 % Allowed : 15.88 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4076 helix: -0.57 (0.12), residues: 1808 sheet: -0.58 (0.24), residues: 536 loop : -1.29 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 835 TYR 0.017 0.002 TYR D 531 PHE 0.019 0.002 PHE B 863 TRP 0.017 0.002 TRP D 84 HIS 0.007 0.002 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (32724) covalent geometry : angle 0.67729 / 0.34 (44328) hydrogen bonds : bond 0.03892 / 2.61 ( 1241) hydrogen bonds : angle 4.69482 / 3.29 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 437 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6947 (mtp-110) cc_final: 0.6306 (mtt90) REVERT: A 103 LYS cc_start: 0.7184 (ptmt) cc_final: 0.6520 (ttpp) REVERT: A 202 ILE cc_start: 0.8689 (mt) cc_final: 0.8167 (pt) REVERT: A 928 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8878 (mt) REVERT: A 1057 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 1060 ILE cc_start: 0.8910 (tp) cc_final: 0.8511 (tp) REVERT: B 65 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6293 (mtt90) REVERT: B 103 LYS cc_start: 0.7221 (ptmt) cc_final: 0.6559 (ttpp) REVERT: B 202 ILE cc_start: 0.8653 (mt) cc_final: 0.8155 (pt) REVERT: B 233 TRP cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (m-10) REVERT: B 516 ASP cc_start: 0.7460 (m-30) cc_final: 0.7237 (m-30) REVERT: B 1057 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 1060 ILE cc_start: 0.8955 (tp) cc_final: 0.8546 (tp) REVERT: C 65 ARG cc_start: 0.6791 (mtp-110) cc_final: 0.6319 (mtt90) REVERT: C 103 LYS cc_start: 0.7208 (ptmt) cc_final: 0.6521 (ttpp) REVERT: C 202 ILE cc_start: 0.8587 (mt) cc_final: 0.8130 (pt) REVERT: C 233 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8726 (m-10) REVERT: C 1057 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8420 (mp) REVERT: C 1060 ILE cc_start: 0.8912 (tp) cc_final: 0.8500 (tp) REVERT: D 65 ARG cc_start: 0.6860 (mtp-110) cc_final: 0.6348 (mtt90) REVERT: D 103 LYS cc_start: 0.7174 (ptmt) cc_final: 0.6507 (ttpt) REVERT: D 202 ILE cc_start: 0.8679 (mt) cc_final: 0.8235 (pt) REVERT: D 1060 ILE cc_start: 0.8931 (tp) cc_final: 0.8532 (tp) outliers start: 65 outliers final: 35 residues processed: 470 average time/residue: 0.2062 time to fit residues: 158.6103 Evaluate side-chains 425 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 384 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 10 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B1098 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132266 restraints weight = 115595.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132694 restraints weight = 96766.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132612 restraints weight = 48066.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132435 restraints weight = 41608.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133080 restraints weight = 37121.764| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32724 Z= 0.122 Angle : 0.603 9.719 44328 Z= 0.297 Chirality : 0.045 0.177 4916 Planarity : 0.004 0.057 5656 Dihedral : 5.773 111.139 4496 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.65 % Allowed : 16.26 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4076 helix: -0.21 (0.12), residues: 1812 sheet: -0.58 (0.23), residues: 560 loop : -1.07 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 788 TYR 0.015 0.002 TYR D 319 PHE 0.015 0.001 PHE A 533 TRP 0.015 0.001 TRP D 84 HIS 0.007 0.001 HIS B1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (32724) covalent geometry : angle 0.60288 / 0.30 (44328) hydrogen bonds : bond 0.03314 / 2.22 ( 1241) hydrogen bonds : angle 4.38648 / 3.08 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 449 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7061 (mtp-110) cc_final: 0.6293 (mtt90) REVERT: A 202 ILE cc_start: 0.8784 (mt) cc_final: 0.8199 (pt) REVERT: A 669 GLU cc_start: 0.7085 (tp30) cc_final: 0.6884 (tp30) REVERT: A 1057 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 1060 ILE cc_start: 0.8864 (tp) cc_final: 0.8457 (tp) REVERT: B 65 ARG cc_start: 0.7030 (mtp-110) cc_final: 0.6284 (mtt90) REVERT: B 103 LYS cc_start: 0.7401 (ptmt) cc_final: 0.6691 (ttpp) REVERT: B 202 ILE cc_start: 0.8771 (mt) cc_final: 0.8159 (pt) REVERT: B 233 TRP cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: B 292 ILE cc_start: 0.8362 (mm) cc_final: 0.7997 (mt) REVERT: B 512 MET cc_start: 0.8450 (mmm) cc_final: 0.7908 (mtt) REVERT: B 847 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 1057 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 1060 ILE cc_start: 0.8870 (tp) cc_final: 0.8482 (tp) REVERT: C 65 ARG cc_start: 0.6939 (mtp-110) cc_final: 0.6291 (mtt90) REVERT: C 202 ILE cc_start: 0.8770 (mt) cc_final: 0.8192 (pt) REVERT: C 233 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8608 (m-10) REVERT: C 292 ILE cc_start: 0.8346 (mm) cc_final: 0.8005 (mt) REVERT: C 512 MET cc_start: 0.8445 (mmm) cc_final: 0.7923 (mtt) REVERT: C 1057 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 1060 ILE cc_start: 0.8908 (tp) cc_final: 0.8526 (tp) REVERT: D 65 ARG cc_start: 0.6981 (mtp-110) cc_final: 0.6318 (mtt90) REVERT: D 202 ILE cc_start: 0.8827 (mt) cc_final: 0.8292 (pt) REVERT: D 292 ILE cc_start: 0.8449 (mm) cc_final: 0.8049 (mp) REVERT: D 512 MET cc_start: 0.8412 (mmm) cc_final: 0.7852 (mtt) REVERT: D 1060 ILE cc_start: 0.8890 (tp) cc_final: 0.8502 (tp) outliers start: 56 outliers final: 35 residues processed: 480 average time/residue: 0.1986 time to fit residues: 158.1888 Evaluate side-chains 437 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 397 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 169 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B 671 ASN ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS C 671 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128307 restraints weight = 109349.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128992 restraints weight = 89350.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128533 restraints weight = 48662.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128573 restraints weight = 37916.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128996 restraints weight = 38154.638| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32724 Z= 0.183 Angle : 0.645 10.718 44328 Z= 0.320 Chirality : 0.047 0.220 4916 Planarity : 0.005 0.055 5656 Dihedral : 5.800 101.011 4496 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.94 % Allowed : 16.50 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4076 helix: -0.22 (0.12), residues: 1816 sheet: -0.37 (0.24), residues: 536 loop : -1.12 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 735 TYR 0.027 0.002 TYR C 227 PHE 0.015 0.002 PHE B 863 TRP 0.024 0.002 TRP A 84 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (32724) covalent geometry : angle 0.64487 / 0.32 (44328) hydrogen bonds : bond 0.03620 / 2.42 ( 1241) hydrogen bonds : angle 4.52417 / 3.16 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7158 (mtp-110) cc_final: 0.6395 (mtt90) REVERT: A 103 LYS cc_start: 0.7265 (ptmt) cc_final: 0.6667 (ttpt) REVERT: A 202 ILE cc_start: 0.8795 (mt) cc_final: 0.8203 (pt) REVERT: A 847 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8009 (mt-10) REVERT: A 1060 ILE cc_start: 0.8855 (tp) cc_final: 0.8457 (tp) REVERT: B 65 ARG cc_start: 0.7150 (mtp-110) cc_final: 0.6342 (mtt90) REVERT: B 103 LYS cc_start: 0.7451 (ptmt) cc_final: 0.6883 (ttpt) REVERT: B 202 ILE cc_start: 0.8829 (mt) cc_final: 0.8257 (pt) REVERT: B 512 MET cc_start: 0.8490 (mmm) cc_final: 0.8090 (mtt) REVERT: B 1060 ILE cc_start: 0.8863 (tp) cc_final: 0.8458 (tp) REVERT: C 65 ARG cc_start: 0.7022 (mtp-110) cc_final: 0.6330 (mtt90) REVERT: C 103 LYS cc_start: 0.7403 (ptmt) cc_final: 0.6825 (ttpt) REVERT: C 202 ILE cc_start: 0.8827 (mt) cc_final: 0.8272 (pt) REVERT: C 233 TRP cc_start: 0.8971 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: C 512 MET cc_start: 0.8485 (mmm) cc_final: 0.8030 (mtt) REVERT: C 1057 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 1060 ILE cc_start: 0.8966 (tp) cc_final: 0.8566 (tp) REVERT: D 65 ARG cc_start: 0.7096 (mtp-110) cc_final: 0.6410 (mtt90) REVERT: D 103 LYS cc_start: 0.7375 (ptmt) cc_final: 0.6773 (ttpt) REVERT: D 202 ILE cc_start: 0.8797 (mt) cc_final: 0.8252 (pt) REVERT: D 512 MET cc_start: 0.8462 (mmm) cc_final: 0.8070 (mtt) REVERT: D 1060 ILE cc_start: 0.8917 (tp) cc_final: 0.8507 (tp) outliers start: 66 outliers final: 52 residues processed: 439 average time/residue: 0.2034 time to fit residues: 147.9147 Evaluate side-chains 435 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 198 optimal weight: 0.1980 chunk 329 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 221 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 278 optimal weight: 0.0010 overall best weight: 0.8408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132453 restraints weight = 107453.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132981 restraints weight = 85430.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132098 restraints weight = 51322.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132830 restraints weight = 36410.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133276 restraints weight = 31873.365| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32724 Z= 0.120 Angle : 0.613 10.865 44328 Z= 0.301 Chirality : 0.047 0.365 4916 Planarity : 0.004 0.045 5656 Dihedral : 5.410 90.643 4494 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.68 % Allowed : 16.91 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4076 helix: 0.06 (0.12), residues: 1804 sheet: -0.52 (0.23), residues: 588 loop : -0.96 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 788 TYR 0.024 0.002 TYR C 227 PHE 0.015 0.001 PHE B 110 TRP 0.022 0.001 TRP A 84 HIS 0.006 0.001 HIS C 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32724) covalent geometry : angle 0.61310 / 0.30 (44328) hydrogen bonds : bond 0.03216 / 2.15 ( 1241) hydrogen bonds : angle 4.33527 / 3.04 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 428 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7122 (mtp-110) cc_final: 0.6446 (mtt90) REVERT: A 103 LYS cc_start: 0.7180 (ptmt) cc_final: 0.6537 (ttpt) REVERT: A 198 THR cc_start: 0.8844 (p) cc_final: 0.8623 (m) REVERT: A 202 ILE cc_start: 0.8805 (mt) cc_final: 0.8251 (pt) REVERT: A 669 GLU cc_start: 0.7134 (tp30) cc_final: 0.6831 (tp30) REVERT: A 847 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 925 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 928 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 1060 ILE cc_start: 0.8940 (tp) cc_final: 0.8536 (tp) REVERT: B 65 ARG cc_start: 0.7041 (mtp-110) cc_final: 0.6385 (mtt90) REVERT: B 103 LYS cc_start: 0.7358 (ptmt) cc_final: 0.6785 (ttpt) REVERT: B 202 ILE cc_start: 0.8742 (mt) cc_final: 0.8172 (pt) REVERT: B 370 GLU cc_start: 0.5049 (pp20) cc_final: 0.4121 (pt0) REVERT: B 512 MET cc_start: 0.8428 (mmm) cc_final: 0.7707 (mtt) REVERT: B 1060 ILE cc_start: 0.8883 (tp) cc_final: 0.8492 (tp) REVERT: C 65 ARG cc_start: 0.7044 (mtp-110) cc_final: 0.6382 (mtt90) REVERT: C 103 LYS cc_start: 0.7347 (ptmt) cc_final: 0.6771 (ttpt) REVERT: C 202 ILE cc_start: 0.8749 (mt) cc_final: 0.8203 (pt) REVERT: C 512 MET cc_start: 0.8450 (mmm) cc_final: 0.7818 (mtt) REVERT: C 847 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 1057 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8632 (mt) REVERT: C 1060 ILE cc_start: 0.8883 (tp) cc_final: 0.8523 (tp) REVERT: D 65 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.6403 (mtt90) REVERT: D 103 LYS cc_start: 0.7331 (ptmt) cc_final: 0.6730 (ttpt) REVERT: D 198 THR cc_start: 0.8830 (p) cc_final: 0.8629 (m) REVERT: D 202 ILE cc_start: 0.8735 (mt) cc_final: 0.8204 (pt) REVERT: D 512 MET cc_start: 0.8450 (mmm) cc_final: 0.7799 (mtt) REVERT: D 847 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8008 (mt-10) REVERT: D 1060 ILE cc_start: 0.8718 (tp) cc_final: 0.8365 (tp) outliers start: 57 outliers final: 43 residues processed: 465 average time/residue: 0.2031 time to fit residues: 157.5644 Evaluate side-chains 448 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 389 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131910 restraints weight = 98337.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133838 restraints weight = 111766.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138933 restraints weight = 56147.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138624 restraints weight = 31235.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139956 restraints weight = 26704.560| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32724 Z= 0.146 Angle : 0.622 11.795 44328 Z= 0.304 Chirality : 0.046 0.219 4916 Planarity : 0.004 0.048 5656 Dihedral : 5.344 83.796 4492 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.41 % Allowed : 17.44 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4076 helix: 0.15 (0.12), residues: 1796 sheet: -0.47 (0.23), residues: 588 loop : -0.92 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 788 TYR 0.016 0.002 TYR B 319 PHE 0.014 0.002 PHE A 533 TRP 0.021 0.001 TRP A 84 HIS 0.006 0.001 HIS C 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (32724) covalent geometry : angle 0.62170 / 0.30 (44328) hydrogen bonds : bond 0.03384 / 2.27 ( 1241) hydrogen bonds : angle 4.37123 / 3.06 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 411 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6541 (mtt90) REVERT: A 103 LYS cc_start: 0.7060 (ptmt) cc_final: 0.6522 (ttpt) REVERT: A 202 ILE cc_start: 0.8689 (mt) cc_final: 0.8169 (pt) REVERT: A 669 GLU cc_start: 0.7015 (tp30) cc_final: 0.6683 (tp30) REVERT: A 847 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 928 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (mt) REVERT: A 1060 ILE cc_start: 0.8917 (tp) cc_final: 0.8494 (tp) REVERT: B 65 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6392 (mtt90) REVERT: B 103 LYS cc_start: 0.7253 (ptmt) cc_final: 0.6698 (ttpt) REVERT: B 202 ILE cc_start: 0.8677 (mt) cc_final: 0.8162 (pt) REVERT: B 370 GLU cc_start: 0.4999 (pp20) cc_final: 0.4046 (pt0) REVERT: B 512 MET cc_start: 0.8424 (mmm) cc_final: 0.7777 (mtt) REVERT: B 847 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 1060 ILE cc_start: 0.8946 (tp) cc_final: 0.8534 (tp) REVERT: C 65 ARG cc_start: 0.6864 (mtp-110) cc_final: 0.6324 (mtt90) REVERT: C 103 LYS cc_start: 0.7239 (ptmt) cc_final: 0.6692 (ttpt) REVERT: C 202 ILE cc_start: 0.8668 (mt) cc_final: 0.8183 (pt) REVERT: C 512 MET cc_start: 0.8431 (mmm) cc_final: 0.7839 (mtt) REVERT: C 847 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 1057 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (mt) REVERT: C 1060 ILE cc_start: 0.8916 (tp) cc_final: 0.8525 (tp) REVERT: D 65 ARG cc_start: 0.6967 (mtp-110) cc_final: 0.6469 (mtt90) REVERT: D 103 LYS cc_start: 0.7173 (ptmt) cc_final: 0.6582 (ttpt) REVERT: D 198 THR cc_start: 0.8805 (p) cc_final: 0.8551 (m) REVERT: D 202 ILE cc_start: 0.8673 (mt) cc_final: 0.8194 (pt) REVERT: D 512 MET cc_start: 0.8457 (mmm) cc_final: 0.7812 (mtt) REVERT: D 847 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8007 (mt-10) REVERT: D 1060 ILE cc_start: 0.8879 (tp) cc_final: 0.8466 (tp) outliers start: 48 outliers final: 41 residues processed: 443 average time/residue: 0.2032 time to fit residues: 149.9885 Evaluate side-chains 442 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 399 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 327 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 362 optimal weight: 0.3980 chunk 256 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 308 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133010 restraints weight = 92451.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133946 restraints weight = 99267.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137120 restraints weight = 60955.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138238 restraints weight = 36910.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139030 restraints weight = 31650.660| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32724 Z= 0.134 Angle : 0.625 13.231 44328 Z= 0.304 Chirality : 0.046 0.215 4916 Planarity : 0.004 0.052 5656 Dihedral : 5.229 79.043 4492 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.38 % Allowed : 17.68 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 4076 helix: 0.26 (0.12), residues: 1796 sheet: -0.44 (0.23), residues: 588 loop : -0.89 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 788 TYR 0.016 0.002 TYR A 319 PHE 0.018 0.001 PHE C 110 TRP 0.020 0.001 TRP A 84 HIS 0.005 0.001 HIS C 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (32724) covalent geometry : angle 0.62549 / 0.30 (44328) hydrogen bonds : bond 0.03262 / 2.18 ( 1241) hydrogen bonds : angle 4.32546 / 3.03 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7051 (mtp-110) cc_final: 0.6588 (mtt90) REVERT: A 103 LYS cc_start: 0.7033 (ptmt) cc_final: 0.6493 (ttpt) REVERT: A 198 THR cc_start: 0.8852 (p) cc_final: 0.8595 (m) REVERT: A 202 ILE cc_start: 0.8736 (mt) cc_final: 0.8204 (pt) REVERT: A 224 THR cc_start: 0.8591 (p) cc_final: 0.8149 (t) REVERT: A 669 GLU cc_start: 0.6904 (tp30) cc_final: 0.6568 (tp30) REVERT: A 847 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 925 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8752 (m) REVERT: A 928 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 1060 ILE cc_start: 0.8877 (tp) cc_final: 0.8451 (tp) REVERT: B 65 ARG cc_start: 0.6963 (mtp-110) cc_final: 0.6477 (mtt90) REVERT: B 103 LYS cc_start: 0.7254 (ptmt) cc_final: 0.6714 (ttpt) REVERT: B 202 ILE cc_start: 0.8674 (mt) cc_final: 0.8168 (pt) REVERT: B 224 THR cc_start: 0.8433 (p) cc_final: 0.8030 (t) REVERT: B 370 GLU cc_start: 0.4979 (pp20) cc_final: 0.4032 (pt0) REVERT: B 512 MET cc_start: 0.8431 (mmm) cc_final: 0.7777 (mtt) REVERT: B 603 GLU cc_start: 0.6953 (mp0) cc_final: 0.6716 (mp0) REVERT: B 767 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.4752 (mp10) REVERT: B 847 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 925 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8601 (m) REVERT: B 1060 ILE cc_start: 0.8883 (tp) cc_final: 0.8448 (tp) REVERT: C 65 ARG cc_start: 0.6734 (mtp-110) cc_final: 0.6282 (mtt90) REVERT: C 103 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6709 (ttpt) REVERT: C 202 ILE cc_start: 0.8670 (mt) cc_final: 0.8182 (pt) REVERT: C 224 THR cc_start: 0.8407 (p) cc_final: 0.7964 (t) REVERT: C 512 MET cc_start: 0.8346 (mmm) cc_final: 0.7774 (mtt) REVERT: C 823 MET cc_start: 0.8938 (ttm) cc_final: 0.8671 (ttp) REVERT: C 847 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 1057 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 1060 ILE cc_start: 0.8869 (tp) cc_final: 0.8464 (tp) REVERT: D 65 ARG cc_start: 0.6964 (mtp-110) cc_final: 0.6533 (mtt90) REVERT: D 103 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6587 (ttpt) REVERT: D 198 THR cc_start: 0.8768 (p) cc_final: 0.8528 (m) REVERT: D 202 ILE cc_start: 0.8674 (mt) cc_final: 0.8187 (pt) REVERT: D 224 THR cc_start: 0.8459 (p) cc_final: 0.8012 (t) REVERT: D 512 MET cc_start: 0.8415 (mmm) cc_final: 0.7738 (mtt) REVERT: D 847 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 1060 ILE cc_start: 0.8917 (tp) cc_final: 0.8488 (tp) outliers start: 47 outliers final: 41 residues processed: 444 average time/residue: 0.2059 time to fit residues: 152.6818 Evaluate side-chains 451 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 405 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 912 ILE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1057 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 385 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 349 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132717 restraints weight = 101546.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134725 restraints weight = 108705.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138900 restraints weight = 55265.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139300 restraints weight = 32346.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140626 restraints weight = 27451.708| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.331 32724 Z= 0.218 Angle : 0.738 59.179 44328 Z= 0.381 Chirality : 0.049 1.269 4916 Planarity : 0.004 0.052 5656 Dihedral : 5.229 79.042 4492 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.50 % Allowed : 17.71 % Favored : 80.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 4076 helix: 0.26 (0.12), residues: 1796 sheet: -0.44 (0.23), residues: 588 loop : -0.89 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 788 TYR 0.016 0.002 TYR A 319 PHE 0.018 0.001 PHE C 110 TRP 0.019 0.001 TRP A 84 HIS 0.005 0.001 HIS C 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (32724) covalent geometry : angle 0.73778 / 0.38 (44328) hydrogen bonds : bond 0.03273 / 2.19 ( 1241) hydrogen bonds : angle 4.32562 / 3.03 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.80 seconds wall clock time: 105 minutes 51.30 seconds (6351.30 seconds total)