Starting phenix.real_space_refine on Mon Jul 6 04:19:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ed8_28032/07_2026/8ed8_28032.cif" } resolution = 3.2 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= -0.001 sd= 0.087 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 232 5.16 5 Na 1 4.78 5 C 20916 2.51 5 N 5376 2.21 5 O 5688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32229 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7841 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 968, 7841 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 38, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {' NA': 1, '3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PH': 1, '9Z9': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE A 913 " occ=0.47 residue: pdb=" N AMET A1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET A1011 " occ=0.57 residue: pdb=" N APHE B 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE B 913 " occ=0.47 residue: pdb=" N AMET B1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET B1011 " occ=0.57 residue: pdb=" N APHE C 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE C 913 " occ=0.47 residue: pdb=" N AMET C1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET C1011 " occ=0.57 residue: pdb=" N APHE D 913 " occ=0.47 ... (9 atoms not shown) pdb=" CZ APHE D 913 " occ=0.47 residue: pdb=" N AMET D1011 " occ=0.57 ... (6 atoms not shown) pdb=" CE AMET D1011 " occ=0.57 Time building chain proxies: 5.79, per 1000 atoms: 0.18 Number of scatterers: 32229 At special positions: 0 Unit cell: (137.16, 137.16, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 16 15.00 Na 1 11.00 O 5688 8.00 N 5376 7.00 C 20916 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 8 sheets defined 66.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.615A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.617A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.994A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.889A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.569A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.515A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.950A pdb=" N ASN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.740A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.566A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.867A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.809A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 643 " --> pdb=" O HIS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.897A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.555A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 removed outlier: 3.558A pdb=" N ALA A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.504A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.518A pdb=" N GLY A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 790 removed outlier: 3.555A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 940 removed outlier: 3.714A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.574A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.225A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 3.924A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1054 removed outlier: 3.527A pdb=" N LYS A1044 " --> pdb=" O TRP A1040 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 4.093A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1105 removed outlier: 4.168A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1118 through 1143 removed outlier: 4.493A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A1143 " --> pdb=" O THR A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.793A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 Processing helix chain 'A' and resid 1215 through 1240 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.616A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.627A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.004A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.023A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.620A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 4.147A pdb=" N THR B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.247A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.946A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.756A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.649A pdb=" N LYS B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.569A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.865A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 3.940A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.881A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 690 through 717 Processing helix chain 'B' and resid 717 through 725 removed outlier: 3.576A pdb=" N ALA B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.509A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.521A pdb=" N GLY B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.543A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.845A pdb=" N VAL B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.584A pdb=" N VAL B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.352A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.859A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1033 removed outlier: 3.827A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.890A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 4.031A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1105 removed outlier: 4.118A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B1097 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1117 Processing helix chain 'B' and resid 1118 through 1143 removed outlier: 4.660A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1163 removed outlier: 3.783A pdb=" N VAL B1163 " --> pdb=" O ILE B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.507A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.608A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.633A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.518A pdb=" N ILE C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 259 " --> pdb=" O TRP C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.932A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.186A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.506A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 4.216A pdb=" N LYS C 401 " --> pdb=" O THR C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.932A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.745A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.588A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.804A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.812A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 643 " --> pdb=" O HIS C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.899A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 removed outlier: 3.792A pdb=" N GLN C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 removed outlier: 3.567A pdb=" N ALA C 721 " --> pdb=" O ASP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.510A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.529A pdb=" N GLY C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 784 through 790 removed outlier: 3.567A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.623A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.225A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1033 removed outlier: 3.748A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1044 Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 3.990A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.121A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C1097 " --> pdb=" O ALA C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1117 Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.675A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1163 removed outlier: 3.790A pdb=" N VAL C1163 " --> pdb=" O ILE C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 Processing helix chain 'C' and resid 1215 through 1240 Processing helix chain 'D' and resid 165 through 175 removed outlier: 3.503A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.867A pdb=" N LYS D 207 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.850A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.999A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.914A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.544A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 removed outlier: 4.129A pdb=" N THR D 402 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 439 through 453 removed outlier: 3.506A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.746A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.588A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 removed outlier: 3.866A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.800A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 643 " --> pdb=" O HIS D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.874A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 689 through 717 removed outlier: 3.736A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 removed outlier: 3.563A pdb=" N ALA D 721 " --> pdb=" O ASP D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.506A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 765 removed outlier: 3.529A pdb=" N GLY D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 790 removed outlier: 5.819A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 790 " --> pdb=" O ILE D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 Processing helix chain 'D' and resid 941 through 962 removed outlier: 3.632A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.359A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.856A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 3.901A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D1027 " --> pdb=" O SER D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1046 removed outlier: 3.784A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1053 Processing helix chain 'D' and resid 1089 through 1105 removed outlier: 4.123A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1096 " --> pdb=" O PRO D1092 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS D1097 " --> pdb=" O ALA D1093 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU D1099 " --> pdb=" O MET D1095 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D1100 " --> pdb=" O ALA D1096 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D1105 " --> pdb=" O VAL D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1117 Processing helix chain 'D' and resid 1118 through 1143 removed outlier: 4.670A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.772A pdb=" N VAL D1163 " --> pdb=" O ILE D1159 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 275 removed outlier: 3.553A pdb=" N GLU A 145 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 218 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 251 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 184 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE A 221 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 362 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 336 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N CYS A 364 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 275 removed outlier: 8.258A pdb=" N PHE B 294 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET B 156 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 296 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 158 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP B 298 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 160 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA B 218 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 251 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE B 220 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 253 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 184 " --> pdb=" O TRP B 219 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE B 221 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 275 removed outlier: 7.159A pdb=" N ALA C 218 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 184 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE C 221 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 361 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE C 430 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 363 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 275 removed outlier: 8.025A pdb=" N PHE D 294 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET D 156 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU D 296 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL D 158 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ASP D 298 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 160 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA D 218 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE D 251 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU D 184 " --> pdb=" O TRP D 219 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE D 221 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL D 339 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N HIS D 189 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) 1740 hydrogen bonds defined for protein. 5127 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: 5.31 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 16 1.05 - 1.26: 5064 1.26 - 1.47: 12969 1.47 - 1.69: 14491 1.69 - 1.90: 428 Bond restraints: 32968 Sorted by residual: bond pdb=" C03 9Z9 D1402 " pdb=" C74 9Z9 D1402 " ideal model delta sigma weight residual 1.534 0.832 0.702 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 C1402 " pdb=" C74 9Z9 C1402 " ideal model delta sigma weight residual 1.534 0.833 0.701 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 B1402 " pdb=" C74 9Z9 B1402 " ideal model delta sigma weight residual 1.534 0.833 0.701 2.00e-02 2.50e+03 1.23e+03 bond pdb=" C03 9Z9 A1402 " pdb=" C74 9Z9 A1402 " ideal model delta sigma weight residual 1.534 0.834 0.700 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 B1402 " pdb=" C03 9Z9 B1402 " ideal model delta sigma weight residual 1.544 1.012 0.532 2.00e-02 2.50e+03 7.07e+02 ... (remaining 32963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.37: 44556 10.37 - 20.74: 12 20.74 - 31.12: 8 31.12 - 41.49: 4 41.49 - 51.86: 4 Bond angle restraints: 44584 Sorted by residual: angle pdb=" C74 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" C76 9Z9 A1402 " ideal model delta sigma weight residual 114.05 165.91 -51.86 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C74 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" C76 9Z9 B1402 " ideal model delta sigma weight residual 114.05 165.72 -51.67 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C74 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" C76 9Z9 C1402 " ideal model delta sigma weight residual 114.05 165.68 -51.63 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C74 9Z9 D1402 " pdb=" C73 9Z9 D1402 " pdb=" C76 9Z9 D1402 " ideal model delta sigma weight residual 114.05 165.59 -51.54 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C76 9Z9 A1402 " pdb=" C73 9Z9 A1402 " pdb=" O72 9Z9 A1402 " ideal model delta sigma weight residual 109.02 70.01 39.01 3.00e+00 1.11e-01 1.69e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.51: 18999 26.51 - 53.03: 599 53.03 - 79.54: 53 79.54 - 106.05: 0 106.05 - 132.57: 4 Dihedral angle restraints: 19655 sinusoidal: 8163 harmonic: 11492 Sorted by residual: dihedral pdb=" CA GLN D1062 " pdb=" C GLN D1062 " pdb=" N ILE D1063 " pdb=" CA ILE D1063 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP C1061 " pdb=" C ASP C1061 " pdb=" N GLN C1062 " pdb=" CA GLN C1062 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 19652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 4968 0.392 - 0.784: 4 0.784 - 1.175: 4 1.175 - 1.567: 0 1.567 - 1.959: 4 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C03 9Z9 D1402 " pdb=" C02 9Z9 D1402 " pdb=" C04 9Z9 D1402 " pdb=" C74 9Z9 D1402 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.59e+01 chirality pdb=" C03 9Z9 B1402 " pdb=" C02 9Z9 B1402 " pdb=" C04 9Z9 B1402 " pdb=" C74 9Z9 B1402 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.59e+01 chirality pdb=" C03 9Z9 A1402 " pdb=" C02 9Z9 A1402 " pdb=" C04 9Z9 A1402 " pdb=" C74 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.57e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " 0.036 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 785 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 784 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 785 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 785 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 785 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 785 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " -0.030 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7352 2.79 - 3.32: 30807 3.32 - 3.85: 50778 3.85 - 4.37: 58548 4.37 - 4.90: 104226 Nonbonded interactions: 251711 Sorted by model distance: nonbonded pdb=" OD1 ASP B 947 " pdb=" OH TYR B 981 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR C 157 " pdb=" O LEU C 265 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR B 157 " pdb=" O LEU B 265 " model vdw 2.285 3.040 nonbonded pdb=" OE2 GLU B 565 " pdb=" OG1 THR B 577 " model vdw 2.304 3.040 ... (remaining 251706 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 129 through 1403) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.750 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 23.830 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.015 0.702 32968 Z= 0.752 Angle : 1.022 51.859 44584 Z= 0.400 Chirality : 0.076 1.959 4980 Planarity : 0.004 0.053 5516 Dihedral : 12.358 132.568 12223 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.56 % Allowed : 6.00 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.14), residues: 3824 helix: 1.14 (0.11), residues: 2392 sheet: 0.90 (0.40), residues: 208 loop : -1.75 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1206 TYR 0.013 0.001 TYR A1098 PHE 0.009 0.001 PHE A 503 TRP 0.012 0.001 TRP A 763 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.01515 / 0.75 (32968) covalent geometry : angle 1.02249 / 0.40 (44584) hydrogen bonds : bond 0.14659 / 9.78 ( 1740) hydrogen bonds : angle 4.79337 / 3.42 ( 5127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 518 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 227 THR cc_start: 0.8017 (p) cc_final: 0.7816 (p) REVERT: A 642 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7224 (tpt) REVERT: B 202 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7449 (ptmm) REVERT: B 642 MET cc_start: 0.7961 (tpt) cc_final: 0.7170 (tpt) REVERT: B 1233 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6833 (ttm110) REVERT: C 202 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7364 (ptmm) REVERT: C 266 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8098 (mm) REVERT: C 340 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5751 (tm-30) REVERT: C 412 HIS cc_start: 0.2778 (OUTLIER) cc_final: 0.2529 (m170) REVERT: D 642 MET cc_start: 0.7976 (tpt) cc_final: 0.7142 (tpt) REVERT: D 1047 PHE cc_start: 0.7870 (t80) cc_final: 0.7588 (m-80) outliers start: 88 outliers final: 24 residues processed: 590 average time/residue: 0.1804 time to fit residues: 170.5294 Evaluate side-chains 412 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 1063 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 291 HIS A 411 GLN A 548 ASN A 633 HIS A 639 HIS A 697 HIS A 719 GLN A 739 GLN A 746 HIS A 978 ASN A 993 ASN A1115 ASN A1116 ASN A1161 GLN A1242 HIS B 203 GLN B 291 HIS B 378 HIS B 411 GLN B 697 HIS B 719 GLN B 739 GLN B 746 HIS B 794 ASN B 940 GLN B1115 ASN B1116 ASN B1161 GLN C 411 GLN C 639 HIS C 697 HIS C 719 GLN C 739 GLN C 746 HIS C 940 GLN C 978 ASN C 993 ASN C1115 ASN C1116 ASN C1161 GLN C1242 HIS D 232 HIS D 291 HIS D 378 HIS D 411 GLN D 639 HIS D 697 HIS D 719 GLN D 739 GLN D 746 HIS D 940 GLN D 978 ASN D 993 ASN D1115 ASN D1116 ASN D1161 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118159 restraints weight = 39628.187| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.32 r_work: 0.3203 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32968 Z= 0.157 Angle : 0.557 9.003 44584 Z= 0.278 Chirality : 0.039 0.167 4980 Planarity : 0.004 0.055 5516 Dihedral : 9.253 127.218 4555 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.24 % Allowed : 9.96 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3824 helix: 1.50 (0.11), residues: 2444 sheet: 0.77 (0.39), residues: 208 loop : -1.78 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 354 TYR 0.011 0.001 TYR A1098 PHE 0.015 0.001 PHE A 162 TRP 0.014 0.001 TRP A 763 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (32968) covalent geometry : angle 0.55718 / 0.28 (44584) hydrogen bonds : bond 0.05225 / 3.44 ( 1740) hydrogen bonds : angle 3.69927 / 2.62 ( 5127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 418 time to evaluate : 0.846 Fit side-chains REVERT: A 192 LEU cc_start: 0.8622 (mt) cc_final: 0.8410 (mt) REVERT: A 397 VAL cc_start: 0.6592 (OUTLIER) cc_final: 0.6303 (p) REVERT: A 462 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 1084 CYS cc_start: 0.8582 (t) cc_final: 0.8360 (p) REVERT: B 154 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8408 (mppt) REVERT: B 281 MET cc_start: 0.7567 (mpp) cc_final: 0.5952 (tmm) REVERT: B 351 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: B 462 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8227 (mp) REVERT: B 642 MET cc_start: 0.8576 (tpt) cc_final: 0.7814 (tpt) REVERT: B 1233 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6612 (ttm110) REVERT: C 412 HIS cc_start: 0.3412 (OUTLIER) cc_final: 0.2479 (m170) REVERT: C 462 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 1057 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: C 1062 GLN cc_start: 0.8097 (mp10) cc_final: 0.7797 (tm-30) REVERT: D 281 MET cc_start: 0.7626 (mpp) cc_final: 0.5967 (tmm) REVERT: D 462 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8181 (mp) REVERT: D 514 MET cc_start: 0.8436 (tpp) cc_final: 0.8213 (mmm) REVERT: D 768 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.6760 (mtt-85) REVERT: D 1047 PHE cc_start: 0.8051 (t80) cc_final: 0.7282 (m-80) outliers start: 77 outliers final: 41 residues processed: 467 average time/residue: 0.1756 time to fit residues: 134.9470 Evaluate side-chains 443 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 393 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A1115 ASN B 203 GLN B 291 HIS B 940 GLN B1115 ASN C1115 ASN ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 940 GLN D1115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114181 restraints weight = 39833.361| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.31 r_work: 0.3208 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 32968 Z= 0.203 Angle : 0.562 7.665 44584 Z= 0.283 Chirality : 0.040 0.194 4980 Planarity : 0.004 0.044 5516 Dihedral : 8.985 124.556 4531 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.13 % Allowed : 10.98 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3824 helix: 1.56 (0.11), residues: 2440 sheet: 0.45 (0.38), residues: 212 loop : -1.76 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 354 TYR 0.014 0.001 TYR A1098 PHE 0.018 0.002 PHE A 162 TRP 0.017 0.001 TRP D 763 HIS 0.005 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (32968) covalent geometry : angle 0.56249 / 0.28 (44584) hydrogen bonds : bond 0.05575 / 3.66 ( 1740) hydrogen bonds : angle 3.67552 / 2.61 ( 5127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 415 time to evaluate : 1.218 Fit side-chains REVERT: A 172 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7936 (tp) REVERT: A 397 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6365 (p) REVERT: A 432 MET cc_start: 0.7203 (mtp) cc_final: 0.6950 (mtp) REVERT: A 462 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 154 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8413 (mppt) REVERT: B 266 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7771 (mm) REVERT: B 281 MET cc_start: 0.7693 (mpp) cc_final: 0.6055 (tmm) REVERT: B 351 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7451 (tp30) REVERT: B 462 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 559 ASP cc_start: 0.8317 (m-30) cc_final: 0.8050 (m-30) REVERT: B 768 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7548 (mtt-85) REVERT: B 925 MET cc_start: 0.7528 (mtt) cc_final: 0.7245 (tmm) REVERT: B 1008 ILE cc_start: 0.8745 (mt) cc_final: 0.8464 (mt) REVERT: B 1233 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6697 (ttm110) REVERT: C 243 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7665 (mttt) REVERT: C 266 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7590 (mm) REVERT: C 340 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: C 412 HIS cc_start: 0.3467 (OUTLIER) cc_final: 0.2571 (m170) REVERT: C 462 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 1062 GLN cc_start: 0.8120 (mp10) cc_final: 0.7855 (tm-30) REVERT: D 281 MET cc_start: 0.7710 (mpp) cc_final: 0.6059 (tmm) REVERT: D 462 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 514 MET cc_start: 0.8474 (tpp) cc_final: 0.8193 (mmm) REVERT: D 1047 PHE cc_start: 0.8098 (t80) cc_final: 0.7345 (m-80) outliers start: 73 outliers final: 35 residues processed: 460 average time/residue: 0.1717 time to fit residues: 130.4941 Evaluate side-chains 445 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 978 ASN Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 285 optimal weight: 0.6980 chunk 303 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B1115 ASN C 318 HIS C 940 GLN C1115 ASN D1115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114760 restraints weight = 39074.268| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.33 r_work: 0.3181 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32968 Z= 0.133 Angle : 0.513 9.523 44584 Z= 0.256 Chirality : 0.038 0.169 4980 Planarity : 0.004 0.042 5516 Dihedral : 8.636 119.031 4525 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.33 % Allowed : 11.41 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.14), residues: 3824 helix: 1.77 (0.11), residues: 2444 sheet: 0.68 (0.38), residues: 208 loop : -1.68 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 354 TYR 0.011 0.001 TYR A 981 PHE 0.016 0.001 PHE B 162 TRP 0.013 0.001 TRP D 763 HIS 0.003 0.000 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (32968) covalent geometry : angle 0.51272 / 0.26 (44584) hydrogen bonds : bond 0.04777 / 3.13 ( 1740) hydrogen bonds : angle 3.48840 / 2.47 ( 5127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 413 time to evaluate : 1.240 Fit side-chains REVERT: A 172 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 264 ASP cc_start: 0.7237 (t0) cc_final: 0.6844 (t0) REVERT: A 397 VAL cc_start: 0.6662 (OUTLIER) cc_final: 0.6385 (p) REVERT: A 432 MET cc_start: 0.7222 (mtp) cc_final: 0.7003 (mtp) REVERT: B 154 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8362 (mppt) REVERT: B 266 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7610 (mm) REVERT: B 281 MET cc_start: 0.7673 (mpp) cc_final: 0.6022 (tmm) REVERT: B 340 GLU cc_start: 0.6776 (tt0) cc_final: 0.6415 (tt0) REVERT: B 642 MET cc_start: 0.8382 (tpt) cc_final: 0.7558 (tpt) REVERT: B 768 ARG cc_start: 0.7680 (mtt-85) cc_final: 0.7407 (mtt-85) REVERT: B 1008 ILE cc_start: 0.8523 (mt) cc_final: 0.8210 (mt) REVERT: B 1162 HIS cc_start: 0.5069 (t70) cc_final: 0.4806 (t-90) REVERT: B 1233 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6512 (ttm110) REVERT: C 243 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7550 (mttt) REVERT: C 264 ASP cc_start: 0.7207 (t0) cc_final: 0.6705 (t0) REVERT: C 266 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7540 (mm) REVERT: C 340 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: C 412 HIS cc_start: 0.3324 (OUTLIER) cc_final: 0.2499 (m170) REVERT: C 1062 GLN cc_start: 0.7987 (mp10) cc_final: 0.7684 (tm-30) REVERT: D 281 MET cc_start: 0.7697 (mpp) cc_final: 0.6025 (tmm) REVERT: D 514 MET cc_start: 0.8290 (tpp) cc_final: 0.8076 (mmm) REVERT: D 642 MET cc_start: 0.8379 (tpt) cc_final: 0.7478 (tpt) REVERT: D 768 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.6880 (mtt-85) REVERT: D 1047 PHE cc_start: 0.7875 (t80) cc_final: 0.7187 (m-80) outliers start: 80 outliers final: 40 residues processed: 465 average time/residue: 0.1699 time to fit residues: 131.2756 Evaluate side-chains 443 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 396 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 115 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 278 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 375 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 746 HIS B1115 ASN C 746 HIS C1115 ASN D 746 HIS D1115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113167 restraints weight = 39703.145| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.38 r_work: 0.3202 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 32968 Z= 0.191 Angle : 0.552 13.013 44584 Z= 0.275 Chirality : 0.040 0.177 4980 Planarity : 0.004 0.043 5516 Dihedral : 8.517 115.513 4521 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.30 % Allowed : 11.76 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.14), residues: 3824 helix: 1.73 (0.11), residues: 2440 sheet: 0.49 (0.38), residues: 212 loop : -1.69 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.013 0.001 TYR A1098 PHE 0.021 0.001 PHE D 162 TRP 0.016 0.001 TRP C 763 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (32968) covalent geometry : angle 0.55161 / 0.28 (44584) hydrogen bonds : bond 0.05321 / 3.49 ( 1740) hydrogen bonds : angle 3.55417 / 2.52 ( 5127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 415 time to evaluate : 1.099 Fit side-chains REVERT: A 172 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 397 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.6434 (p) REVERT: A 432 MET cc_start: 0.7317 (mtp) cc_final: 0.7072 (mtp) REVERT: A 489 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: B 154 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8369 (mppt) REVERT: B 264 ASP cc_start: 0.7312 (t0) cc_final: 0.6842 (t0) REVERT: B 266 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7650 (mm) REVERT: B 281 MET cc_start: 0.7675 (mpp) cc_final: 0.6023 (tmm) REVERT: B 340 GLU cc_start: 0.6882 (tt0) cc_final: 0.6628 (tt0) REVERT: B 862 ARG cc_start: 0.6377 (tpt170) cc_final: 0.6112 (tpt170) REVERT: B 1008 ILE cc_start: 0.8651 (mt) cc_final: 0.8357 (mt) REVERT: B 1162 HIS cc_start: 0.5104 (t70) cc_final: 0.4855 (t-90) REVERT: B 1233 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6596 (ttm110) REVERT: C 243 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7522 (mttt) REVERT: C 264 ASP cc_start: 0.7296 (t0) cc_final: 0.6822 (t0) REVERT: C 266 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7543 (mm) REVERT: C 340 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: C 412 HIS cc_start: 0.3453 (OUTLIER) cc_final: 0.2540 (m170) REVERT: C 1062 GLN cc_start: 0.8015 (mp10) cc_final: 0.7721 (tm-30) REVERT: D 243 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7597 (mttt) REVERT: D 281 MET cc_start: 0.7692 (mpp) cc_final: 0.6038 (tmm) REVERT: D 445 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (mp) REVERT: D 514 MET cc_start: 0.8351 (tpp) cc_final: 0.8111 (mmm) REVERT: D 768 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.6956 (mtt-85) REVERT: D 1047 PHE cc_start: 0.7894 (t80) cc_final: 0.7219 (m-80) outliers start: 79 outliers final: 40 residues processed: 468 average time/residue: 0.1708 time to fit residues: 131.7081 Evaluate side-chains 450 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 401 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 67 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 171 HIS B1115 ASN C1115 ASN D1115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.160601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113627 restraints weight = 39652.307| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.40 r_work: 0.3208 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32968 Z= 0.167 Angle : 0.544 12.967 44584 Z= 0.269 Chirality : 0.039 0.154 4980 Planarity : 0.004 0.043 5516 Dihedral : 8.363 111.392 4520 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.42 % Allowed : 12.46 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.14), residues: 3824 helix: 1.76 (0.11), residues: 2444 sheet: 0.51 (0.38), residues: 212 loop : -1.69 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.011 0.001 TYR A1098 PHE 0.019 0.001 PHE D 162 TRP 0.015 0.001 TRP A 763 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (32968) covalent geometry : angle 0.54407 / 0.27 (44584) hydrogen bonds : bond 0.05119 / 3.36 ( 1740) hydrogen bonds : angle 3.51084 / 2.49 ( 5127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 420 time to evaluate : 1.080 Fit side-chains REVERT: A 172 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 264 ASP cc_start: 0.7298 (t0) cc_final: 0.6959 (t0) REVERT: A 397 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.6476 (p) REVERT: A 432 MET cc_start: 0.7375 (mtp) cc_final: 0.7125 (mtp) REVERT: A 489 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: B 154 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8369 (mppt) REVERT: B 197 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 264 ASP cc_start: 0.7331 (t0) cc_final: 0.6895 (t0) REVERT: B 266 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7687 (mm) REVERT: B 281 MET cc_start: 0.7638 (mpp) cc_final: 0.6132 (tmm) REVERT: B 340 GLU cc_start: 0.6838 (tt0) cc_final: 0.6590 (tt0) REVERT: B 1008 ILE cc_start: 0.8638 (mt) cc_final: 0.8344 (mt) REVERT: B 1162 HIS cc_start: 0.5139 (t70) cc_final: 0.4893 (t-90) REVERT: B 1233 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6640 (ttm110) REVERT: C 243 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7506 (mttt) REVERT: C 264 ASP cc_start: 0.7394 (t0) cc_final: 0.6775 (t0) REVERT: C 266 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7543 (mm) REVERT: C 340 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: C 412 HIS cc_start: 0.3478 (OUTLIER) cc_final: 0.2549 (m170) REVERT: C 1062 GLN cc_start: 0.8002 (mp10) cc_final: 0.7700 (tm-30) REVERT: D 243 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7586 (mttt) REVERT: D 281 MET cc_start: 0.7652 (mpp) cc_final: 0.6123 (tmm) REVERT: D 530 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7630 (mmt90) REVERT: D 768 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.6984 (mtt-85) REVERT: D 1047 PHE cc_start: 0.7895 (t80) cc_final: 0.7226 (m-80) outliers start: 83 outliers final: 49 residues processed: 477 average time/residue: 0.1755 time to fit residues: 136.3687 Evaluate side-chains 460 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 402 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 210 optimal weight: 5.9990 chunk 270 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS A 291 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 291 HIS B1115 ASN C1115 ASN D1115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113272 restraints weight = 40077.903| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.49 r_work: 0.3203 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32968 Z= 0.161 Angle : 0.541 15.541 44584 Z= 0.269 Chirality : 0.039 0.139 4980 Planarity : 0.004 0.044 5516 Dihedral : 8.254 106.967 4520 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.36 % Allowed : 12.52 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.14), residues: 3824 helix: 1.77 (0.11), residues: 2448 sheet: 0.51 (0.37), residues: 212 loop : -1.68 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 530 TYR 0.010 0.001 TYR A1098 PHE 0.027 0.001 PHE D 162 TRP 0.015 0.001 TRP C 763 HIS 0.006 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (32968) covalent geometry : angle 0.54105 / 0.27 (44584) hydrogen bonds : bond 0.05033 / 3.30 ( 1740) hydrogen bonds : angle 3.48318 / 2.47 ( 5127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 420 time to evaluate : 1.056 Fit side-chains REVERT: A 172 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 264 ASP cc_start: 0.7333 (t0) cc_final: 0.7048 (t0) REVERT: A 281 MET cc_start: 0.7672 (mpp) cc_final: 0.6205 (tmm) REVERT: A 432 MET cc_start: 0.7419 (mtp) cc_final: 0.7155 (mtp) REVERT: A 489 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6521 (mt-10) REVERT: A 1094 ILE cc_start: 0.8716 (mt) cc_final: 0.8426 (mm) REVERT: B 154 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8346 (mppt) REVERT: B 197 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 264 ASP cc_start: 0.7296 (t0) cc_final: 0.6855 (t0) REVERT: B 266 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7673 (mm) REVERT: B 281 MET cc_start: 0.7675 (mpp) cc_final: 0.6176 (tmm) REVERT: B 340 GLU cc_start: 0.6824 (tt0) cc_final: 0.6611 (tt0) REVERT: B 940 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7846 (mm110) REVERT: B 1008 ILE cc_start: 0.8597 (mt) cc_final: 0.8295 (mt) REVERT: B 1162 HIS cc_start: 0.5115 (t70) cc_final: 0.4858 (t-90) REVERT: B 1233 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6570 (ttm110) REVERT: C 243 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7499 (mttt) REVERT: C 264 ASP cc_start: 0.7263 (t0) cc_final: 0.6826 (t0) REVERT: C 266 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7518 (mm) REVERT: C 340 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: C 412 HIS cc_start: 0.3361 (OUTLIER) cc_final: 0.2474 (m170) REVERT: C 1062 GLN cc_start: 0.8076 (mp10) cc_final: 0.7700 (tm-30) REVERT: D 173 MET cc_start: 0.7743 (mtp) cc_final: 0.7519 (mtp) REVERT: D 243 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7564 (mttt) REVERT: D 268 ARG cc_start: 0.6930 (mpt180) cc_final: 0.6630 (mmt-90) REVERT: D 281 MET cc_start: 0.7697 (mpp) cc_final: 0.6177 (tmm) REVERT: D 530 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7633 (mmt90) REVERT: D 768 ARG cc_start: 0.7656 (mtp-110) cc_final: 0.6973 (mtt-85) REVERT: D 1047 PHE cc_start: 0.7897 (t80) cc_final: 0.7216 (m-80) outliers start: 81 outliers final: 50 residues processed: 474 average time/residue: 0.1763 time to fit residues: 136.4071 Evaluate side-chains 471 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 413 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 331 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 151 HIS B 291 HIS B1115 ASN C 151 HIS C 940 GLN C1115 ASN D1115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112744 restraints weight = 39810.085| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.41 r_work: 0.3200 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32968 Z= 0.189 Angle : 0.568 18.072 44584 Z= 0.281 Chirality : 0.040 0.159 4980 Planarity : 0.004 0.044 5516 Dihedral : 8.217 103.141 4520 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.24 % Allowed : 12.93 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.14), residues: 3824 helix: 1.71 (0.11), residues: 2444 sheet: 0.57 (0.37), residues: 208 loop : -1.72 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.012 0.001 TYR A1098 PHE 0.030 0.001 PHE A 162 TRP 0.016 0.001 TRP C 763 HIS 0.004 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (32968) covalent geometry : angle 0.56774 / 0.28 (44584) hydrogen bonds : bond 0.05304 / 3.48 ( 1740) hydrogen bonds : angle 3.53122 / 2.50 ( 5127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 419 time to evaluate : 0.772 Fit side-chains REVERT: A 172 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 264 ASP cc_start: 0.7356 (t0) cc_final: 0.6806 (t0) REVERT: A 281 MET cc_start: 0.7658 (mpp) cc_final: 0.6266 (tmm) REVERT: A 432 MET cc_start: 0.7458 (mtp) cc_final: 0.7194 (mtp) REVERT: A 489 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: A 530 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7712 (mmt90) REVERT: A 1081 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6159 (mt) REVERT: A 1094 ILE cc_start: 0.8736 (mt) cc_final: 0.8451 (mm) REVERT: B 154 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8374 (mppt) REVERT: B 197 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7928 (mp) REVERT: B 264 ASP cc_start: 0.7351 (t0) cc_final: 0.6940 (t0) REVERT: B 266 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7704 (mm) REVERT: B 281 MET cc_start: 0.7668 (mpp) cc_final: 0.6248 (tmm) REVERT: B 925 MET cc_start: 0.6951 (mtt) cc_final: 0.6661 (tmm) REVERT: B 1008 ILE cc_start: 0.8648 (mt) cc_final: 0.8368 (mt) REVERT: B 1081 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6264 (mt) REVERT: B 1162 HIS cc_start: 0.5127 (t70) cc_final: 0.4875 (t-90) REVERT: B 1233 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6633 (ttm110) REVERT: C 243 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7506 (mttt) REVERT: C 264 ASP cc_start: 0.7316 (t0) cc_final: 0.6895 (t0) REVERT: C 266 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7498 (mm) REVERT: C 340 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: C 412 HIS cc_start: 0.3513 (OUTLIER) cc_final: 0.2579 (m170) REVERT: C 925 MET cc_start: 0.7177 (mtt) cc_final: 0.6794 (tmm) REVERT: C 1062 GLN cc_start: 0.8086 (mp10) cc_final: 0.7681 (tm-30) REVERT: D 243 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7562 (mttt) REVERT: D 268 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6507 (mmt-90) REVERT: D 281 MET cc_start: 0.7763 (mpp) cc_final: 0.6254 (tmm) REVERT: D 354 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7578 (mtt90) REVERT: D 530 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7655 (mmt90) REVERT: D 925 MET cc_start: 0.7007 (mtt) cc_final: 0.6661 (tmm) REVERT: D 1047 PHE cc_start: 0.7914 (t80) cc_final: 0.7248 (m-80) outliers start: 77 outliers final: 55 residues processed: 473 average time/residue: 0.1725 time to fit residues: 133.1133 Evaluate side-chains 469 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 404 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1081 LEU Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 30 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 chunk 352 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 249 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 291 HIS B 940 GLN B1115 ASN C 291 HIS C1115 ASN D 151 HIS D 940 GLN D1115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115352 restraints weight = 39421.049| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.40 r_work: 0.3239 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32968 Z= 0.123 Angle : 0.520 10.085 44584 Z= 0.259 Chirality : 0.038 0.142 4980 Planarity : 0.004 0.083 5516 Dihedral : 7.995 98.647 4520 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.95 % Allowed : 13.36 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.14), residues: 3824 helix: 1.88 (0.11), residues: 2448 sheet: 0.70 (0.38), residues: 208 loop : -1.68 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 530 TYR 0.012 0.001 TYR A 981 PHE 0.027 0.001 PHE A 162 TRP 0.014 0.001 TRP D 763 HIS 0.005 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (32968) covalent geometry : angle 0.52043 / 0.26 (44584) hydrogen bonds : bond 0.04613 / 3.03 ( 1740) hydrogen bonds : angle 3.41182 / 2.42 ( 5127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 0.865 Fit side-chains REVERT: A 172 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 264 ASP cc_start: 0.7337 (t0) cc_final: 0.6869 (t0) REVERT: A 281 MET cc_start: 0.7621 (mpp) cc_final: 0.6175 (tmm) REVERT: A 432 MET cc_start: 0.7473 (mtp) cc_final: 0.7215 (mtp) REVERT: A 489 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: A 530 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7719 (mmt90) REVERT: A 642 MET cc_start: 0.8235 (tpp) cc_final: 0.6979 (tpt) REVERT: A 925 MET cc_start: 0.6682 (mtt) cc_final: 0.6462 (tmm) REVERT: A 1081 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6223 (mt) REVERT: A 1094 ILE cc_start: 0.8689 (mt) cc_final: 0.8405 (mm) REVERT: B 154 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8424 (mppt) REVERT: B 197 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7878 (mp) REVERT: B 264 ASP cc_start: 0.7285 (t0) cc_final: 0.6911 (t0) REVERT: B 266 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7688 (mm) REVERT: B 281 MET cc_start: 0.7647 (mpp) cc_final: 0.6242 (tmm) REVERT: B 642 MET cc_start: 0.8468 (tpt) cc_final: 0.7633 (tpt) REVERT: B 925 MET cc_start: 0.6957 (mtt) cc_final: 0.6692 (tmm) REVERT: B 1008 ILE cc_start: 0.8515 (mt) cc_final: 0.8181 (mt) REVERT: B 1081 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6243 (mt) REVERT: B 1162 HIS cc_start: 0.5118 (t70) cc_final: 0.4878 (t-90) REVERT: B 1233 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6588 (ttm110) REVERT: C 264 ASP cc_start: 0.7284 (t0) cc_final: 0.6905 (t0) REVERT: C 266 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7547 (mm) REVERT: C 340 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: C 412 HIS cc_start: 0.3356 (OUTLIER) cc_final: 0.2454 (m170) REVERT: C 642 MET cc_start: 0.8209 (tpp) cc_final: 0.6967 (tpt) REVERT: C 925 MET cc_start: 0.7053 (mtt) cc_final: 0.6713 (tmm) REVERT: C 1062 GLN cc_start: 0.7999 (mp10) cc_final: 0.7633 (tm-30) REVERT: D 243 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7554 (mttt) REVERT: D 268 ARG cc_start: 0.6947 (mpt180) cc_final: 0.6627 (mmt-90) REVERT: D 281 MET cc_start: 0.7755 (mpp) cc_final: 0.6254 (tmm) REVERT: D 530 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7639 (mmt90) REVERT: D 925 MET cc_start: 0.6850 (mtt) cc_final: 0.6572 (tmm) REVERT: D 1047 PHE cc_start: 0.7889 (t80) cc_final: 0.7208 (m-80) outliers start: 67 outliers final: 49 residues processed: 469 average time/residue: 0.1768 time to fit residues: 135.9593 Evaluate side-chains 474 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 415 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 179 optimal weight: 0.0060 chunk 203 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 291 HIS B1115 ASN C 291 HIS C1115 ASN D 151 HIS D 291 HIS D1115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.158975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113529 restraints weight = 39398.299| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32968 Z= 0.177 Angle : 0.556 10.206 44584 Z= 0.276 Chirality : 0.040 0.161 4980 Planarity : 0.004 0.080 5516 Dihedral : 7.957 95.434 4520 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.83 % Allowed : 13.68 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.14), residues: 3824 helix: 1.77 (0.11), residues: 2448 sheet: 0.51 (0.37), residues: 212 loop : -1.70 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 272 TYR 0.012 0.001 TYR A1098 PHE 0.034 0.001 PHE C 162 TRP 0.015 0.001 TRP C 763 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (32968) covalent geometry : angle 0.55567 / 0.28 (44584) hydrogen bonds : bond 0.05090 / 3.34 ( 1740) hydrogen bonds : angle 3.48479 / 2.47 ( 5127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 416 time to evaluate : 1.042 Fit side-chains REVERT: A 172 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 264 ASP cc_start: 0.7280 (t0) cc_final: 0.6817 (t0) REVERT: A 281 MET cc_start: 0.7629 (mpp) cc_final: 0.6225 (tmm) REVERT: A 432 MET cc_start: 0.7474 (mtp) cc_final: 0.7211 (mtp) REVERT: A 489 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: A 530 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7738 (mmt90) REVERT: A 642 MET cc_start: 0.8263 (tpp) cc_final: 0.7016 (tpt) REVERT: A 925 MET cc_start: 0.6805 (mtt) cc_final: 0.6492 (tmm) REVERT: A 1081 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6176 (mt) REVERT: A 1094 ILE cc_start: 0.8730 (mt) cc_final: 0.8447 (mm) REVERT: B 154 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8430 (mppt) REVERT: B 197 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 264 ASP cc_start: 0.7322 (t0) cc_final: 0.6931 (t0) REVERT: B 266 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7615 (mm) REVERT: B 281 MET cc_start: 0.7761 (mpp) cc_final: 0.6270 (tmm) REVERT: B 925 MET cc_start: 0.6996 (mtt) cc_final: 0.6684 (tmm) REVERT: B 1008 ILE cc_start: 0.8577 (mt) cc_final: 0.8257 (mt) REVERT: B 1081 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6271 (mt) REVERT: B 1162 HIS cc_start: 0.5131 (t70) cc_final: 0.4885 (t-90) REVERT: B 1233 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6596 (ttm110) REVERT: C 264 ASP cc_start: 0.7275 (t0) cc_final: 0.6946 (t0) REVERT: C 266 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7497 (mm) REVERT: C 340 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: C 412 HIS cc_start: 0.3518 (OUTLIER) cc_final: 0.2554 (m170) REVERT: C 642 MET cc_start: 0.8225 (tpp) cc_final: 0.6966 (tpt) REVERT: C 925 MET cc_start: 0.7254 (mtt) cc_final: 0.6786 (tmm) REVERT: C 1062 GLN cc_start: 0.8039 (mp10) cc_final: 0.7650 (tm-30) REVERT: D 243 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7570 (mttt) REVERT: D 268 ARG cc_start: 0.6998 (mpt180) cc_final: 0.6646 (mmt-90) REVERT: D 281 MET cc_start: 0.7772 (mpp) cc_final: 0.6265 (tmm) REVERT: D 530 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7660 (mmt90) REVERT: D 925 MET cc_start: 0.7095 (mtt) cc_final: 0.6730 (tmm) REVERT: D 1047 PHE cc_start: 0.7901 (t80) cc_final: 0.7220 (m-80) outliers start: 63 outliers final: 48 residues processed: 458 average time/residue: 0.1756 time to fit residues: 131.7415 Evaluate side-chains 469 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 411 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1233 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 531 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 579 LYS Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 212 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 178 optimal weight: 0.0670 chunk 223 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 291 HIS B1115 ASN C 203 GLN C 291 HIS C1115 ASN D 151 HIS D 291 HIS D1115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115699 restraints weight = 39053.793| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.32 r_work: 0.3192 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32968 Z= 0.117 Angle : 0.518 10.962 44584 Z= 0.257 Chirality : 0.038 0.152 4980 Planarity : 0.004 0.078 5516 Dihedral : 7.791 91.374 4520 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.98 % Allowed : 13.68 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.14), residues: 3824 helix: 1.94 (0.11), residues: 2448 sheet: 0.76 (0.38), residues: 208 loop : -1.65 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 272 TYR 0.012 0.001 TYR A 981 PHE 0.029 0.001 PHE C 162 TRP 0.014 0.001 TRP C 763 HIS 0.004 0.000 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (32968) covalent geometry : angle 0.51775 / 0.26 (44584) hydrogen bonds : bond 0.04501 / 2.95 ( 1740) hydrogen bonds : angle 3.37703 / 2.40 ( 5127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6408.54 seconds wall clock time: 110 minutes 43.03 seconds (6643.03 seconds total)