Starting phenix.real_space_refine on Fri Mar 6 15:11:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o0h_0567/03_2026/6o0h_0567.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0h_0567/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6o0h_0567/03_2026/6o0h_0567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0h_0567/03_2026/6o0h_0567.map" model { file = "/net/cci-nas-00/data/ceres_data/6o0h_0567/03_2026/6o0h_0567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0h_0567/03_2026/6o0h_0567.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 12.65, per 1000 atoms: 0.40 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: 2.57 Conformation dependent library (CDL) restraints added in 2.4 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: 1.54 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: 7.88 Time building geometry restraints manager: 3.46 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: 19325 34.94 - 69.89: 169 69.89 - 104.83: 16 104.83 - 139.77: 4 139.77 - 174.71: 2 Dihedral angle restraints: 19516 sinusoidal: 7852 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 19513 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: 0.08 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.570 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 10.835 174.713 12108 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 covalent geometry : bond 0.00885 (32724) covalent geometry : angle 1.16492 (44328) hydrogen bonds : bond 0.17440 ( 1241) hydrogen bonds : angle 7.64492 ( 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 : 1.284 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: 0.2292 time to fit residues: 345.0864 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 : 1.177 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.168250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139572 restraints weight = 101938.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142605 restraints weight = 120882.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146049 restraints weight = 52282.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146036 restraints weight = 33523.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147504 restraints weight = 27024.779| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 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 = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2798 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= 0.144 Angle : 0.694 11.704 44328 Z= 0.352 Chirality : 0.048 0.210 4916 Planarity : 0.007 0.071 5656 Dihedral : 8.599 164.317 4540 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.15 % Allowed : 10.71 % 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 covalent geometry : bond 0.00323 (32724) covalent geometry : angle 0.69353 (44328) hydrogen bonds : bond 0.04210 ( 1241) hydrogen bonds : angle 5.10236 ( 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 694 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 621 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6707 (mtp-110) cc_final: 0.6125 (mtt90) REVERT: A 202 ILE cc_start: 0.8349 (mt) cc_final: 0.7811 (pt) REVERT: A 232 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (mmmt) REVERT: A 233 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: A 781 GLU cc_start: 0.7568 (tp30) cc_final: 0.6861 (mt-10) REVERT: A 909 ASN cc_start: 0.7821 (p0) cc_final: 0.7620 (p0) REVERT: A 955 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 1060 ILE cc_start: 0.8827 (tp) cc_final: 0.8455 (tp) REVERT: A 1075 ASP cc_start: 0.8612 (t70) cc_final: 0.8172 (t0) REVERT: B 65 ARG cc_start: 0.6774 (mtp-110) cc_final: 0.6266 (mtt90) REVERT: B 202 ILE cc_start: 0.8307 (mt) cc_final: 0.7794 (pt) REVERT: B 232 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7887 (mmmt) REVERT: B 233 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.8042 (m-10) REVERT: B 955 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8297 (tp) REVERT: B 1060 ILE cc_start: 0.8871 (tp) cc_final: 0.8499 (tp) REVERT: B 1075 ASP cc_start: 0.8639 (t70) cc_final: 0.8171 (t0) REVERT: C 65 ARG cc_start: 0.6778 (mtp-110) cc_final: 0.6295 (mtt90) REVERT: C 202 ILE cc_start: 0.8290 (mt) cc_final: 0.7780 (pt) REVERT: C 232 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (mmmt) REVERT: C 233 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: C 1060 ILE cc_start: 0.8862 (tp) cc_final: 0.8512 (tp) REVERT: C 1075 ASP cc_start: 0.8636 (t70) cc_final: 0.8167 (t0) REVERT: D 65 ARG cc_start: 0.6767 (mtp-110) cc_final: 0.6274 (mtt90) REVERT: D 202 ILE cc_start: 0.8349 (mt) cc_final: 0.7853 (pt) REVERT: D 232 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7865 (mmmt) REVERT: D 233 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.7954 (m-10) REVERT: D 955 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8308 (tp) REVERT: D 1060 ILE cc_start: 0.8871 (tp) cc_final: 0.8503 (tp) REVERT: D 1075 ASP cc_start: 0.8573 (t70) cc_final: 0.8112 (t0) outliers start: 73 outliers final: 36 residues processed: 669 average time/residue: 0.2050 time to fit residues: 219.6325 Evaluate side-chains 502 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 370 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 908 HIS ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.131058 restraints weight = 102358.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130442 restraints weight = 94272.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129788 restraints weight = 51503.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129612 restraints weight = 50082.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130553 restraints weight = 37151.361| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 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 = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 32724 Z= 0.237 Angle : 0.730 11.302 44328 Z= 0.370 Chirality : 0.050 0.204 4916 Planarity : 0.006 0.064 5656 Dihedral : 7.999 151.439 4540 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 13.76 % Favored : 83.94 % 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: -2.06 (0.13), residues: 4076 helix: -1.20 (0.11), residues: 1780 sheet: -0.92 (0.23), residues: 560 loop : -1.54 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 65 TYR 0.018 0.002 TYR B 531 PHE 0.026 0.003 PHE C 863 TRP 0.020 0.002 TRP D 276 HIS 0.007 0.002 HIS B 700 Details of bonding type rmsd covalent geometry : bond 0.00556 (32724) covalent geometry : angle 0.72962 (44328) hydrogen bonds : bond 0.04284 ( 1241) hydrogen bonds : angle 4.98273 ( 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 553 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 475 time to evaluate : 1.243 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: A 36 PRO cc_start: 0.7296 (Cg_exo) cc_final: 0.7086 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6938 (mtp-110) cc_final: 0.6151 (mtt90) REVERT: A 103 LYS cc_start: 0.7945 (ptmt) cc_final: 0.6648 (ttpp) REVERT: A 202 ILE cc_start: 0.8765 (mt) cc_final: 0.8242 (pt) REVERT: A 233 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (m-10) REVERT: A 630 LYS cc_start: 0.8656 (tttt) cc_final: 0.8416 (tttt) REVERT: A 909 ASN cc_start: 0.8282 (p0) cc_final: 0.8046 (p0) REVERT: A 957 MET cc_start: 0.6830 (tpt) cc_final: 0.6624 (tpt) REVERT: A 1060 ILE cc_start: 0.9036 (tp) cc_final: 0.8654 (tp) REVERT: B 13 GLU cc_start: 0.6809 (tt0) cc_final: 0.6604 (tt0) REVERT: B 65 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6118 (mtt90) REVERT: B 103 LYS cc_start: 0.7971 (ptmt) cc_final: 0.6655 (ttpp) REVERT: B 137 GLU cc_start: 0.6951 (tp30) cc_final: 0.6627 (tp30) REVERT: B 202 ILE cc_start: 0.8726 (mt) cc_final: 0.8176 (pt) REVERT: B 233 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8648 (m-10) REVERT: B 630 LYS cc_start: 0.8640 (tttt) cc_final: 0.8385 (tttt) REVERT: B 957 MET cc_start: 0.6830 (tpt) cc_final: 0.6628 (tpt) REVERT: B 1060 ILE cc_start: 0.9017 (tp) cc_final: 0.8622 (tp) REVERT: C 65 ARG cc_start: 0.6852 (mtp-110) cc_final: 0.6193 (mtt90) REVERT: C 103 LYS cc_start: 0.7973 (ptmt) cc_final: 0.6652 (ttpp) REVERT: C 137 GLU cc_start: 0.6942 (tp30) cc_final: 0.6611 (tp30) REVERT: C 202 ILE cc_start: 0.8705 (mt) cc_final: 0.8158 (pt) REVERT: C 233 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.8645 (m-10) REVERT: C 630 LYS cc_start: 0.8630 (tttt) cc_final: 0.8393 (tttt) REVERT: C 1060 ILE cc_start: 0.8927 (tp) cc_final: 0.8525 (tp) REVERT: D 13 GLU cc_start: 0.6792 (tt0) cc_final: 0.6578 (tt0) REVERT: D 36 PRO cc_start: 0.7287 (Cg_exo) cc_final: 0.7072 (Cg_endo) REVERT: D 65 ARG cc_start: 0.6911 (mtp-110) cc_final: 0.6217 (mtt90) REVERT: D 103 LYS cc_start: 0.7971 (ptmt) cc_final: 0.6624 (ttpp) REVERT: D 202 ILE cc_start: 0.8741 (mt) cc_final: 0.8217 (pt) REVERT: D 215 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6863 (tp) REVERT: D 233 TRP cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: D 292 ILE cc_start: 0.8478 (mm) cc_final: 0.8107 (mp) REVERT: D 327 MET cc_start: 0.6654 (mmm) cc_final: 0.6393 (mmm) REVERT: D 630 LYS cc_start: 0.8642 (tttt) cc_final: 0.8394 (tttt) REVERT: D 957 MET cc_start: 0.6835 (tpt) cc_final: 0.6632 (tpt) REVERT: D 1060 ILE cc_start: 0.8928 (tp) cc_final: 0.8533 (tp) outliers start: 78 outliers final: 48 residues processed: 518 average time/residue: 0.2030 time to fit residues: 171.1200 Evaluate side-chains 468 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 415 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 618 VAL Chi-restraints excluded: chain A residue 651 LEU 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 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 540 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 651 LEU 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 233 TRP Chi-restraints excluded: chain C residue 304 TYR 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 651 LEU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 923 SER 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 215 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 651 LEU 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: 3.9990 chunk 108 optimal weight: 0.5980 chunk 234 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.0270 chunk 126 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 385 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 421 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS ** C1081 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 = 0.3948 r_free = 0.3948 target = 0.161178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133913 restraints weight = 91472.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138805 restraints weight = 131049.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141379 restraints weight = 42548.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142744 restraints weight = 26982.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143040 restraints weight = 19435.219| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32724 Z= 0.160 Angle : 0.637 10.688 44328 Z= 0.320 Chirality : 0.047 0.175 4916 Planarity : 0.005 0.056 5656 Dihedral : 7.210 143.822 4524 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.74 % Allowed : 14.91 % Favored : 83.35 % 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: -1.62 (0.13), residues: 4076 helix: -0.80 (0.11), residues: 1812 sheet: -0.77 (0.23), residues: 560 loop : -1.33 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 788 TYR 0.017 0.002 TYR A 319 PHE 0.015 0.002 PHE A 863 TRP 0.017 0.001 TRP D 84 HIS 0.007 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00380 (32724) covalent geometry : angle 0.63679 (44328) hydrogen bonds : bond 0.03697 ( 1241) hydrogen bonds : angle 4.70709 ( 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 489 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 430 time to evaluate : 1.227 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: A 36 PRO cc_start: 0.7095 (Cg_exo) cc_final: 0.6887 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6793 (mtp-110) cc_final: 0.6296 (mtt90) REVERT: A 103 LYS cc_start: 0.6970 (ptmt) cc_final: 0.6272 (ttpt) REVERT: A 202 ILE cc_start: 0.8653 (mt) cc_final: 0.8204 (pt) REVERT: A 233 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.8655 (m-10) REVERT: A 512 MET cc_start: 0.8433 (mmm) cc_final: 0.8216 (mtt) REVERT: A 957 MET cc_start: 0.6646 (tpt) cc_final: 0.6442 (tpt) REVERT: B 65 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6268 (mtt90) REVERT: B 103 LYS cc_start: 0.7169 (ptmt) cc_final: 0.6499 (ttpp) REVERT: B 202 ILE cc_start: 0.8615 (mt) cc_final: 0.8164 (pt) REVERT: B 233 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8614 (m-10) REVERT: B 292 ILE cc_start: 0.8316 (mm) cc_final: 0.7965 (mp) REVERT: B 847 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 957 MET cc_start: 0.6638 (tpt) cc_final: 0.6433 (tpt) REVERT: C 65 ARG cc_start: 0.6640 (mtp-110) cc_final: 0.6277 (mtt90) REVERT: C 103 LYS cc_start: 0.7182 (ptmt) cc_final: 0.6515 (ttpp) REVERT: C 202 ILE cc_start: 0.8598 (mt) cc_final: 0.8187 (pt) REVERT: C 233 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.8632 (m-10) REVERT: C 292 ILE cc_start: 0.8389 (mm) cc_final: 0.8037 (mp) REVERT: C 512 MET cc_start: 0.8414 (mmm) cc_final: 0.8182 (mtt) REVERT: C 847 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 65 ARG cc_start: 0.6661 (mtp-110) cc_final: 0.6296 (mtt90) REVERT: D 103 LYS cc_start: 0.6967 (ptmt) cc_final: 0.6259 (ttpt) REVERT: D 202 ILE cc_start: 0.8625 (mt) cc_final: 0.8229 (pt) REVERT: D 233 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: D 512 MET cc_start: 0.8437 (mmm) cc_final: 0.8197 (mtt) REVERT: D 847 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 59 outliers final: 41 residues processed: 465 average time/residue: 0.1974 time to fit residues: 151.2030 Evaluate side-chains 435 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 304 TYR 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 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 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 233 TRP Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET 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: 5.9990 chunk 14 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 368 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.3918 r_free = 0.3918 target = 0.158881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130758 restraints weight = 78709.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133892 restraints weight = 99517.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135852 restraints weight = 55540.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136580 restraints weight = 35340.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138846 restraints weight = 28048.923| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32724 Z= 0.170 Angle : 0.631 10.316 44328 Z= 0.316 Chirality : 0.047 0.289 4916 Planarity : 0.005 0.053 5656 Dihedral : 6.817 136.702 4524 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.15 % Allowed : 15.47 % Favored : 82.38 % 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: -1.32 (0.13), residues: 4076 helix: -0.54 (0.12), residues: 1816 sheet: -0.53 (0.24), residues: 536 loop : -1.22 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 735 TYR 0.015 0.002 TYR A 319 PHE 0.015 0.002 PHE A 189 TRP 0.016 0.001 TRP D 84 HIS 0.006 0.001 HIS D 908 Details of bonding type rmsd covalent geometry : bond 0.00404 (32724) covalent geometry : angle 0.63085 (44328) hydrogen bonds : bond 0.03637 ( 1241) hydrogen bonds : angle 4.60591 ( 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 510 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 437 time to evaluate : 1.230 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: A 36 PRO cc_start: 0.7137 (Cg_exo) cc_final: 0.6917 (Cg_endo) REVERT: A 65 ARG cc_start: 0.6887 (mtp-110) cc_final: 0.6271 (mtt90) REVERT: A 103 LYS cc_start: 0.7305 (ptmt) cc_final: 0.6653 (ttpt) REVERT: A 202 ILE cc_start: 0.8724 (mt) cc_final: 0.8220 (pt) REVERT: A 512 MET cc_start: 0.8439 (mmm) cc_final: 0.7835 (mtt) REVERT: A 847 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 928 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8841 (mt) REVERT: A 957 MET cc_start: 0.6909 (tpt) cc_final: 0.6691 (tpt) REVERT: A 1060 ILE cc_start: 0.8921 (tp) cc_final: 0.8519 (tp) REVERT: B 65 ARG cc_start: 0.6899 (mtp-110) cc_final: 0.6280 (mtt90) REVERT: B 103 LYS cc_start: 0.7288 (ptmt) cc_final: 0.6615 (ttpp) REVERT: B 202 ILE cc_start: 0.8719 (mt) cc_final: 0.8171 (pt) REVERT: B 233 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.8573 (m-10) REVERT: B 847 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 957 MET cc_start: 0.6889 (tpt) cc_final: 0.6662 (tpt) REVERT: B 1060 ILE cc_start: 0.8948 (tp) cc_final: 0.8550 (tp) REVERT: C 65 ARG cc_start: 0.6759 (mtp-110) cc_final: 0.6273 (mtt90) REVERT: C 103 LYS cc_start: 0.7292 (ptmt) cc_final: 0.6614 (ttpp) REVERT: C 202 ILE cc_start: 0.8733 (mt) cc_final: 0.8246 (pt) REVERT: C 233 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: C 512 MET cc_start: 0.8397 (mmm) cc_final: 0.7803 (mtt) REVERT: C 847 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7983 (mt-10) REVERT: C 1060 ILE cc_start: 0.8977 (tp) cc_final: 0.8564 (tp) REVERT: D 65 ARG cc_start: 0.6838 (mtp-110) cc_final: 0.6314 (mtt90) REVERT: D 103 LYS cc_start: 0.7281 (ptmt) cc_final: 0.6616 (ttpt) REVERT: D 202 ILE cc_start: 0.8692 (mt) cc_final: 0.8221 (pt) REVERT: D 512 MET cc_start: 0.8401 (mmm) cc_final: 0.7811 (mtt) REVERT: D 847 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 1060 ILE cc_start: 0.8951 (tp) cc_final: 0.8560 (tp) outliers start: 73 outliers final: 43 residues processed: 474 average time/residue: 0.2059 time to fit residues: 160.4264 Evaluate side-chains 445 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 233 TRP Chi-restraints excluded: chain B residue 304 TYR 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 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 565 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 923 SER 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 534 THR 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 1049 ASP 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: 10.0000 chunk 299 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 374 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131047 restraints weight = 115671.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130921 restraints weight = 101437.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131891 restraints weight = 53268.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131471 restraints weight = 38634.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131991 restraints weight = 34073.995| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4208 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= 0.140 Angle : 0.621 9.843 44328 Z= 0.307 Chirality : 0.047 0.328 4916 Planarity : 0.004 0.049 5656 Dihedral : 6.270 109.684 4520 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.88 % Allowed : 16.03 % 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: -1.07 (0.13), residues: 4076 helix: -0.31 (0.12), residues: 1812 sheet: -0.53 (0.24), 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 A 319 PHE 0.017 0.002 PHE C 134 TRP 0.015 0.001 TRP A 84 HIS 0.008 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00333 (32724) covalent geometry : angle 0.62053 (44328) hydrogen bonds : bond 0.03413 ( 1241) hydrogen bonds : angle 4.46637 ( 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 491 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 427 time to evaluate : 1.285 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: A 36 PRO cc_start: 0.7172 (Cg_exo) cc_final: 0.6918 (Cg_endo) REVERT: A 65 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6301 (mtt90) REVERT: A 103 LYS cc_start: 0.7424 (ptmt) cc_final: 0.6768 (ttpt) REVERT: A 202 ILE cc_start: 0.8795 (mt) cc_final: 0.8220 (pt) REVERT: A 512 MET cc_start: 0.8433 (mmm) cc_final: 0.7929 (mtt) REVERT: A 928 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8789 (mt) REVERT: A 957 MET cc_start: 0.6871 (tpt) cc_final: 0.6624 (tpt) REVERT: A 1060 ILE cc_start: 0.8877 (tp) cc_final: 0.8464 (tp) REVERT: B 65 ARG cc_start: 0.7090 (mtp-110) cc_final: 0.6335 (mtt90) REVERT: B 103 LYS cc_start: 0.7440 (ptmt) cc_final: 0.6798 (ttpt) REVERT: B 198 THR cc_start: 0.8887 (p) cc_final: 0.8677 (m) REVERT: B 202 ILE cc_start: 0.8786 (mt) cc_final: 0.8218 (pt) REVERT: B 292 ILE cc_start: 0.8397 (mm) cc_final: 0.8037 (mt) REVERT: B 512 MET cc_start: 0.8466 (mmm) cc_final: 0.7919 (mtt) REVERT: B 669 GLU cc_start: 0.7148 (tp30) cc_final: 0.6871 (tp30) REVERT: B 847 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 957 MET cc_start: 0.6884 (tpt) cc_final: 0.6632 (tpt) REVERT: B 1060 ILE cc_start: 0.8894 (tp) cc_final: 0.8488 (tp) REVERT: C 65 ARG cc_start: 0.6967 (mtp-110) cc_final: 0.6313 (mtt90) REVERT: C 103 LYS cc_start: 0.7426 (ptmt) cc_final: 0.6784 (ttpt) REVERT: C 202 ILE cc_start: 0.8779 (mt) cc_final: 0.8234 (pt) REVERT: C 512 MET cc_start: 0.8402 (mmm) cc_final: 0.7936 (mtt) REVERT: C 847 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 1060 ILE cc_start: 0.8851 (tp) cc_final: 0.8438 (tp) REVERT: D 65 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.6327 (mtt90) REVERT: D 103 LYS cc_start: 0.7429 (ptmt) cc_final: 0.6752 (ttpt) REVERT: D 202 ILE cc_start: 0.8771 (mt) cc_final: 0.8242 (pt) REVERT: D 512 MET cc_start: 0.8443 (mmm) cc_final: 0.8040 (mtt) REVERT: D 847 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7985 (mt-10) REVERT: D 1060 ILE cc_start: 0.8885 (tp) cc_final: 0.8475 (tp) outliers start: 64 outliers final: 43 residues processed: 464 average time/residue: 0.2087 time to fit residues: 161.0486 Evaluate side-chains 439 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 395 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 492 LEU 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 857 MET 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 344 ILE 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 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 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 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 344 ILE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET 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: 8.9990 chunk 238 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 324 optimal weight: 0.9980 chunk 208 optimal weight: 0.0970 chunk 187 optimal weight: 0.6980 chunk 274 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 671 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130596 restraints weight = 109185.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129979 restraints weight = 87261.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129825 restraints weight = 55698.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130044 restraints weight = 38425.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130644 restraints weight = 34447.210| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4384 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 : 0.600 10.708 44328 Z= 0.295 Chirality : 0.046 0.306 4916 Planarity : 0.004 0.049 5656 Dihedral : 5.920 95.002 4516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 16.26 % Favored : 82.00 % 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: -0.83 (0.13), residues: 4076 helix: -0.07 (0.12), residues: 1796 sheet: -0.45 (0.24), residues: 560 loop : -0.97 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 788 TYR 0.013 0.002 TYR A 319 PHE 0.016 0.002 PHE B 110 TRP 0.024 0.001 TRP A 84 HIS 0.007 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00306 (32724) covalent geometry : angle 0.59950 (44328) hydrogen bonds : bond 0.03284 ( 1241) hydrogen bonds : angle 4.38608 ( 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 491 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 432 time to evaluate : 1.248 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 36 PRO cc_start: 0.7087 (Cg_exo) cc_final: 0.6843 (Cg_endo) REVERT: A 65 ARG cc_start: 0.7112 (mtp-110) cc_final: 0.6408 (mtt90) REVERT: A 103 LYS cc_start: 0.7394 (ptmt) cc_final: 0.6782 (ttpt) REVERT: A 202 ILE cc_start: 0.8802 (mt) cc_final: 0.8223 (pt) REVERT: A 512 MET cc_start: 0.8438 (mmm) cc_final: 0.7812 (mtt) REVERT: A 669 GLU cc_start: 0.7170 (tp30) cc_final: 0.6825 (tp30) REVERT: A 925 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8639 (m) REVERT: A 928 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8667 (mt) REVERT: A 1060 ILE cc_start: 0.8817 (tp) cc_final: 0.8457 (tp) REVERT: B 65 ARG cc_start: 0.7163 (mtp-110) cc_final: 0.6498 (mtt90) REVERT: B 103 LYS cc_start: 0.7503 (ptmt) cc_final: 0.6893 (ttpt) REVERT: B 202 ILE cc_start: 0.8768 (mt) cc_final: 0.8211 (pt) REVERT: B 512 MET cc_start: 0.8467 (mmm) cc_final: 0.7758 (mtt) REVERT: B 669 GLU cc_start: 0.7140 (tp30) cc_final: 0.6795 (tp30) REVERT: B 847 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 1060 ILE cc_start: 0.8898 (tp) cc_final: 0.8513 (tp) REVERT: C 65 ARG cc_start: 0.7016 (mtp-110) cc_final: 0.6370 (mtt90) REVERT: C 103 LYS cc_start: 0.7483 (ptmt) cc_final: 0.6890 (ttpt) REVERT: C 202 ILE cc_start: 0.8809 (mt) cc_final: 0.8252 (pt) REVERT: C 512 MET cc_start: 0.8403 (mmm) cc_final: 0.7777 (mtt) REVERT: C 669 GLU cc_start: 0.7173 (tp30) cc_final: 0.6878 (tp30) REVERT: C 847 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8014 (mt-10) REVERT: C 1060 ILE cc_start: 0.8904 (tp) cc_final: 0.8524 (tp) REVERT: D 65 ARG cc_start: 0.7105 (mtp-110) cc_final: 0.6455 (mtt90) REVERT: D 103 LYS cc_start: 0.7398 (ptmt) cc_final: 0.6788 (ttpt) REVERT: D 202 ILE cc_start: 0.8779 (mt) cc_final: 0.8239 (pt) REVERT: D 512 MET cc_start: 0.8422 (mmm) cc_final: 0.7767 (mtt) REVERT: D 669 GLU cc_start: 0.7153 (tp30) cc_final: 0.6832 (tp30) REVERT: D 847 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7996 (mt-10) REVERT: D 1060 ILE cc_start: 0.8874 (tp) cc_final: 0.8505 (tp) outliers start: 59 outliers final: 43 residues processed: 471 average time/residue: 0.1979 time to fit residues: 155.0771 Evaluate side-chains 447 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 402 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 492 LEU 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 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 811 VAL 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 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 857 MET 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 492 LEU Chi-restraints excluded: chain D residue 534 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 198 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 221 optimal weight: 0.0030 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 671 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 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 D 671 ASN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127771 restraints weight = 107430.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127984 restraints weight = 90940.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128709 restraints weight = 47270.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128318 restraints weight = 34208.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128803 restraints weight = 32229.000| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32724 Z= 0.181 Angle : 0.643 10.945 44328 Z= 0.319 Chirality : 0.047 0.295 4916 Planarity : 0.005 0.057 5656 Dihedral : 6.104 91.099 4516 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.79 % Allowed : 16.79 % 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: -0.87 (0.13), residues: 4076 helix: -0.12 (0.12), residues: 1812 sheet: -0.27 (0.23), residues: 564 loop : -1.07 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 835 TYR 0.014 0.002 TYR C 531 PHE 0.015 0.002 PHE D 863 TRP 0.023 0.002 TRP A 84 HIS 0.004 0.001 HIS C 700 Details of bonding type rmsd covalent geometry : bond 0.00432 (32724) covalent geometry : angle 0.64309 (44328) hydrogen bonds : bond 0.03634 ( 1241) hydrogen bonds : angle 4.52679 ( 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 468 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 407 time to evaluate : 1.192 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: A 36 PRO cc_start: 0.7050 (Cg_exo) cc_final: 0.6844 (Cg_endo) REVERT: A 65 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6544 (mtt90) REVERT: A 103 LYS cc_start: 0.7290 (ptmt) cc_final: 0.6722 (ttpt) REVERT: A 202 ILE cc_start: 0.8828 (mt) cc_final: 0.8267 (pt) REVERT: A 512 MET cc_start: 0.8485 (mmm) cc_final: 0.7803 (mtt) REVERT: A 928 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 1060 ILE cc_start: 0.8883 (tp) cc_final: 0.8519 (tp) REVERT: B 65 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6483 (mtt90) REVERT: B 103 LYS cc_start: 0.7407 (ptmt) cc_final: 0.6815 (ttpp) REVERT: B 202 ILE cc_start: 0.8803 (mt) cc_final: 0.8268 (pt) REVERT: B 370 GLU cc_start: 0.5306 (pp20) cc_final: 0.4476 (pt0) REVERT: B 512 MET cc_start: 0.8527 (mmm) cc_final: 0.7792 (mtt) REVERT: B 847 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 925 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8630 (m) REVERT: B 1060 ILE cc_start: 0.8873 (tp) cc_final: 0.8507 (tp) REVERT: C 65 ARG cc_start: 0.7013 (mtp-110) cc_final: 0.6442 (mtt90) REVERT: C 103 LYS cc_start: 0.7456 (ptmt) cc_final: 0.6868 (ttpp) REVERT: C 202 ILE cc_start: 0.8803 (mt) cc_final: 0.8292 (pt) REVERT: C 512 MET cc_start: 0.8448 (mmm) cc_final: 0.7789 (mtt) REVERT: C 847 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 1060 ILE cc_start: 0.8903 (tp) cc_final: 0.8546 (tp) REVERT: D 65 ARG cc_start: 0.7212 (mtp-110) cc_final: 0.6552 (mtt90) REVERT: D 103 LYS cc_start: 0.7374 (ptmt) cc_final: 0.6804 (ttpt) REVERT: D 202 ILE cc_start: 0.8804 (mt) cc_final: 0.8318 (pt) REVERT: D 512 MET cc_start: 0.8478 (mmm) cc_final: 0.7790 (mtt) REVERT: D 847 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 1060 ILE cc_start: 0.8904 (tp) cc_final: 0.8544 (tp) outliers start: 61 outliers final: 49 residues processed: 445 average time/residue: 0.1972 time to fit residues: 144.5722 Evaluate side-chains 448 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 492 LEU 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 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 304 TYR Chi-restraints excluded: chain B residue 344 ILE 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 719 ILE Chi-restraints excluded: chain B residue 811 VAL 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 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 719 ILE Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 923 SER 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 492 LEU Chi-restraints excluded: chain D residue 534 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 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: 1.9990 chunk 213 optimal weight: 0.0050 chunk 1 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 389 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 282 optimal weight: 0.2980 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS D 496 HIS ** D 908 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.160379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131956 restraints weight = 98279.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134404 restraints weight = 102552.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137738 restraints weight = 53532.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138210 restraints weight = 33236.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139382 restraints weight = 28587.939| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 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 = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4665 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= 0.125 Angle : 0.610 11.334 44328 Z= 0.299 Chirality : 0.046 0.323 4916 Planarity : 0.004 0.059 5656 Dihedral : 5.761 84.110 4516 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.44 % Allowed : 17.56 % Favored : 81.00 % 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: 0.14 (0.12), residues: 1800 sheet: -0.40 (0.23), residues: 588 loop : -0.95 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 788 TYR 0.014 0.001 TYR D1073 PHE 0.017 0.001 PHE B 110 TRP 0.020 0.001 TRP A 84 HIS 0.006 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00298 (32724) covalent geometry : angle 0.60984 (44328) hydrogen bonds : bond 0.03295 ( 1241) hydrogen bonds : angle 4.36029 ( 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 468 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 419 time to evaluate : 1.162 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: symmetry clash revert: symmetry clash REVERT: A 36 PRO cc_start: 0.6933 (Cg_exo) cc_final: 0.6732 (Cg_endo) REVERT: A 65 ARG cc_start: 0.7088 (mtp-110) cc_final: 0.6593 (mtt90) REVERT: A 103 LYS cc_start: 0.7109 (ptmt) cc_final: 0.6531 (ttpt) REVERT: A 198 THR cc_start: 0.8772 (p) cc_final: 0.8528 (m) REVERT: A 202 ILE cc_start: 0.8734 (mt) cc_final: 0.8221 (pt) REVERT: A 512 MET cc_start: 0.8346 (mmm) cc_final: 0.7718 (mtt) REVERT: A 925 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8653 (m) REVERT: A 928 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8675 (mt) REVERT: A 1060 ILE cc_start: 0.8798 (tp) cc_final: 0.8437 (tp) REVERT: B 65 ARG cc_start: 0.6988 (mtp-110) cc_final: 0.6533 (mtt90) REVERT: B 103 LYS cc_start: 0.7251 (ptmt) cc_final: 0.6691 (ttpt) REVERT: B 181 LEU cc_start: 0.7257 (mm) cc_final: 0.7032 (mt) REVERT: B 202 ILE cc_start: 0.8688 (mt) cc_final: 0.8189 (pt) REVERT: B 224 THR cc_start: 0.8570 (p) cc_final: 0.8140 (t) REVERT: B 370 GLU cc_start: 0.5032 (pp20) cc_final: 0.4076 (pt0) REVERT: B 512 MET cc_start: 0.8406 (mmm) cc_final: 0.7721 (mtt) REVERT: B 847 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 925 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 1060 ILE cc_start: 0.8839 (tp) cc_final: 0.8466 (tp) REVERT: C 65 ARG cc_start: 0.6992 (mtp-110) cc_final: 0.6479 (mtt90) REVERT: C 103 LYS cc_start: 0.7294 (ptmt) cc_final: 0.6741 (ttpt) REVERT: C 202 ILE cc_start: 0.8695 (mt) cc_final: 0.8213 (pt) REVERT: C 224 THR cc_start: 0.8594 (p) cc_final: 0.8171 (t) REVERT: C 512 MET cc_start: 0.8316 (mmm) cc_final: 0.7731 (mtt) REVERT: C 669 GLU cc_start: 0.7034 (tp30) cc_final: 0.6714 (tp30) REVERT: C 847 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7964 (mt-10) REVERT: C 1060 ILE cc_start: 0.8809 (tp) cc_final: 0.8426 (tp) REVERT: D 65 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.6547 (mtt90) REVERT: D 103 LYS cc_start: 0.7292 (ptmt) cc_final: 0.6679 (ttpt) REVERT: D 198 THR cc_start: 0.8779 (p) cc_final: 0.8536 (m) REVERT: D 202 ILE cc_start: 0.8659 (mt) cc_final: 0.8188 (pt) REVERT: D 512 MET cc_start: 0.8356 (mmm) cc_final: 0.7707 (mtt) REVERT: D 847 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 1060 ILE cc_start: 0.8823 (tp) cc_final: 0.8451 (tp) outliers start: 49 outliers final: 42 residues processed: 454 average time/residue: 0.1945 time to fit residues: 146.8269 Evaluate side-chains 445 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 400 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 492 LEU 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 811 VAL 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 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 102 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 642 MET 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: 3.9990 chunk 228 optimal weight: 6.9990 chunk 229 optimal weight: 0.0980 chunk 208 optimal weight: 3.9990 chunk 362 optimal weight: 0.0770 chunk 256 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 308 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 146 optimal weight: 3.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 767 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS B 767 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136654 restraints weight = 93516.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142382 restraints weight = 122360.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144251 restraints weight = 38945.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145624 restraints weight = 26514.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145969 restraints weight = 20973.229| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4854 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= 0.107 Angle : 0.604 13.429 44328 Z= 0.293 Chirality : 0.045 0.313 4916 Planarity : 0.004 0.061 5656 Dihedral : 5.368 72.734 4516 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.21 % Allowed : 17.76 % Favored : 81.03 % 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: -0.43 (0.14), residues: 4076 helix: 0.34 (0.12), residues: 1804 sheet: -0.33 (0.23), residues: 588 loop : -0.84 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 788 TYR 0.015 0.001 TYR D1073 PHE 0.016 0.001 PHE B 110 TRP 0.018 0.001 TRP A 84 HIS 0.006 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00251 (32724) covalent geometry : angle 0.60442 (44328) hydrogen bonds : bond 0.03067 ( 1241) hydrogen bonds : angle 4.20077 ( 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 493 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 452 time to evaluate : 1.204 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.6786 (mtp-110) cc_final: 0.6495 (mtt90) REVERT: A 224 THR cc_start: 0.8452 (p) cc_final: 0.8012 (t) REVERT: A 327 MET cc_start: 0.6603 (mmm) cc_final: 0.6328 (mmm) REVERT: A 512 MET cc_start: 0.8236 (mmm) cc_final: 0.7821 (mtt) REVERT: A 767 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.5283 (mp10) REVERT: A 925 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 928 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 957 MET cc_start: 0.5579 (mmm) cc_final: 0.5330 (mmm) REVERT: A 1060 ILE cc_start: 0.8692 (tp) cc_final: 0.8356 (tp) REVERT: B 65 ARG cc_start: 0.6766 (mtp-110) cc_final: 0.6508 (mtt90) REVERT: B 103 LYS cc_start: 0.7120 (ptmt) cc_final: 0.6526 (ttpt) REVERT: B 181 LEU cc_start: 0.7240 (mm) cc_final: 0.7002 (mt) REVERT: B 202 ILE cc_start: 0.8490 (mt) cc_final: 0.8061 (pt) REVERT: B 224 THR cc_start: 0.8440 (p) cc_final: 0.8042 (t) REVERT: B 370 GLU cc_start: 0.4942 (pp20) cc_final: 0.3988 (pt0) REVERT: B 512 MET cc_start: 0.8342 (mmm) cc_final: 0.7786 (mtt) REVERT: B 767 GLN cc_start: 0.5587 (OUTLIER) cc_final: 0.4881 (mp10) REVERT: B 847 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 925 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8570 (m) REVERT: B 957 MET cc_start: 0.5597 (mmm) cc_final: 0.5352 (mmm) REVERT: B 1060 ILE cc_start: 0.8676 (tp) cc_final: 0.8360 (tp) REVERT: C 65 ARG cc_start: 0.6857 (mtp-110) cc_final: 0.6423 (mtt90) REVERT: C 103 LYS cc_start: 0.7329 (ptmt) cc_final: 0.6713 (ttpt) REVERT: C 202 ILE cc_start: 0.8508 (mt) cc_final: 0.8091 (pt) REVERT: C 224 THR cc_start: 0.8487 (p) cc_final: 0.8072 (t) REVERT: C 512 MET cc_start: 0.8218 (mmm) cc_final: 0.7853 (mtt) REVERT: C 669 GLU cc_start: 0.6772 (tp30) cc_final: 0.6486 (tp30) REVERT: C 767 GLN cc_start: 0.5760 (OUTLIER) cc_final: 0.5088 (mp10) REVERT: C 847 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7914 (mt-10) REVERT: C 1060 ILE cc_start: 0.8702 (tp) cc_final: 0.8375 (tp) REVERT: D 65 ARG cc_start: 0.6869 (mtp-110) cc_final: 0.6442 (mtt90) REVERT: D 202 ILE cc_start: 0.8564 (mt) cc_final: 0.8115 (pt) REVERT: D 224 THR cc_start: 0.8452 (p) cc_final: 0.8001 (t) REVERT: D 327 MET cc_start: 0.6612 (mmm) cc_final: 0.6385 (mmm) REVERT: D 512 MET cc_start: 0.8208 (mmm) cc_final: 0.7795 (mtt) REVERT: D 847 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 1060 ILE cc_start: 0.8686 (tp) cc_final: 0.8363 (tp) outliers start: 41 outliers final: 32 residues processed: 481 average time/residue: 0.1966 time to fit residues: 155.6641 Evaluate side-chains 450 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 412 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 767 GLN 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 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 767 GLN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 925 THR 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 767 GLN 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 393 GLU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 565 GLU 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: 1.9990 chunk 33 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 292 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 385 optimal weight: 0.7980 chunk 318 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 GLN ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN D 421 HIS ** D 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.164404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135905 restraints weight = 101980.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138170 restraints weight = 104015.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142072 restraints weight = 52015.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142482 restraints weight = 31680.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143803 restraints weight = 27220.071| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 32724 Z= 0.247 Angle : 0.940 59.200 44328 Z= 0.515 Chirality : 0.059 1.523 4916 Planarity : 0.004 0.061 5656 Dihedral : 5.370 72.745 4516 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.24 % Allowed : 17.91 % Favored : 80.85 % Cbeta Deviations : 0.08 % 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: -0.42 (0.14), residues: 4076 helix: 0.35 (0.12), residues: 1804 sheet: -0.33 (0.23), residues: 588 loop : -0.84 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 788 TYR 0.015 0.001 TYR D1073 PHE 0.016 0.001 PHE A 110 TRP 0.017 0.001 TRP A 84 HIS 0.006 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00547 (32724) covalent geometry : angle 0.93984 (44328) hydrogen bonds : bond 0.03081 ( 1241) hydrogen bonds : angle 4.20950 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5815.29 seconds wall clock time: 101 minutes 30.72 seconds (6090.72 seconds total)