Starting phenix.real_space_refine on Mon Jul 6 04:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ed9_28033/07_2026/8ed9_28033.cif" } resolution = 3.4 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= 0.069 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 1 residue(s): 0.05s 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 dihedrals: 1 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 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: 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: "B" 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: "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: 7.99, per 1000 atoms: 0.25 Number of scatterers: 32229 At special positions: 0 Unit cell: (136.08, 137.16, 159.84, 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 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: 192 helices and 9 sheets defined 66.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.942A pdb=" N GLY A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.649A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.535A 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: 4.176A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.770A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.902A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.540A pdb=" N LYS A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 4.027A pdb=" N GLN A 400 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 401' Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.520A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 4.090A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 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 527 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.509A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.063A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 4.116A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.883A 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 690 through 717 Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.609A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 784 through 790 removed outlier: 3.656A pdb=" N LEU A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 789 " --> pdb=" O SER A 786 " (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: 3.871A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.595A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.382A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 3.911A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) removed outlier: 4.694A 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 1045 removed outlier: 3.813A pdb=" N LYS A1044 " --> pdb=" O TRP A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 4.176A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1105 removed outlier: 4.258A 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 1141 removed outlier: 4.449A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1149 No H-bonds generated for 'chain 'A' and resid 1147 through 1149' Processing helix chain 'A' and resid 1150 through 1163 removed outlier: 4.156A pdb=" N SER A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 removed outlier: 3.509A pdb=" N SER A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1239 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.956A pdb=" N LYS B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.697A pdb=" N HIS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.932A 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: 3.957A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.503A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.755A pdb=" N LYS B 401 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 402' Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.156A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 4.080A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 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 removed outlier: 3.531A pdb=" N ASN B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.505A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 578 through 587 removed outlier: 4.085A pdb=" N ASN B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.128A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.884A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 683 Processing helix chain 'B' and resid 690 through 717 Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.605A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.806A pdb=" N LEU B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 789 " --> pdb=" O SER B 786 " (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: 3.525A pdb=" N LYS B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.671A pdb=" N VAL B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.413A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 4.045A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1033 removed outlier: 3.976A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1055 removed outlier: 3.787A pdb=" N LYS B1044 " --> pdb=" O TRP B1040 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N MET B1049 " --> pdb=" O ASN B1045 " (cutoff:3.500A) Proline residue: B1050 - end of helix removed outlier: 4.060A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1105 removed outlier: 4.293A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) removed outlier: 3.622A 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: 4.701A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1149 No H-bonds generated for 'chain 'B' and resid 1147 through 1149' Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 4.153A pdb=" N SER B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B1163 " --> pdb=" O ILE B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 removed outlier: 3.543A pdb=" N SER B1214 " --> pdb=" O ASP B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1215 through 1240 Processing helix chain 'F' and resid 1 through 5 removed outlier: 3.519A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 198 through 215 removed outlier: 3.574A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.717A pdb=" N HIS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.110A 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 355 removed outlier: 4.300A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.549A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.927A pdb=" N LYS C 401 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 402 " --> pdb=" O ILE C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.555A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.064A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 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: 3.515A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.073A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 4.116A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.877A 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 690 through 717 Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.608A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 765 removed outlier: 3.520A 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: 3.792A pdb=" N LEU C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 789 " --> pdb=" O SER C 786 " (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: 3.568A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 962 " --> pdb=" O MET C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.335A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1033 removed outlier: 3.824A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C1015 " --> pdb=" O AMET C1011 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1045 removed outlier: 3.808A pdb=" N LYS C1044 " --> pdb=" O TRP C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1055 removed outlier: 4.089A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1105 removed outlier: 4.069A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.599A 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 1141 removed outlier: 4.730A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1149 No H-bonds generated for 'chain 'C' and resid 1147 through 1149' Processing helix chain 'C' and resid 1150 through 1163 removed outlier: 4.158A pdb=" N SER C1154 " --> pdb=" O LEU C1150 " (cutoff:3.500A) removed outlier: 3.677A 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 1239 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.759A pdb=" N HIS D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.570A 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 308 through 321 removed outlier: 3.645A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 4.029A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.718A pdb=" N LYS D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 402 " --> pdb=" O ILE D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 398 through 402' Processing helix chain 'D' and resid 413 through 420 Processing helix chain 'D' and resid 439 through 452 Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 4.062A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 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: 3.511A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 577 Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.068A pdb=" N ASN D 587 " --> pdb=" O THR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.984A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.880A 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 690 through 717 Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.598A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 765 removed outlier: 3.558A 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 787 removed outlier: 3.585A pdb=" N ILE D 787 " --> pdb=" O PRO D 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 784 through 787' 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: 3.597A pdb=" N VAL D 945 " --> pdb=" O GLU D 941 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 962 " --> pdb=" O MET D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.438A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.959A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 3.891A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR D1012 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D1027 " --> pdb=" O SER D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1054 removed outlier: 3.828A pdb=" N LYS D1044 " --> pdb=" O TRP D1040 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D1046 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE D1047 " --> pdb=" O ALA D1043 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N MET D1049 " --> pdb=" O ASN D1045 " (cutoff:3.500A) Proline residue: D1050 - end of helix removed outlier: 4.131A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1105 removed outlier: 4.337A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1117 Processing helix chain 'D' and resid 1118 through 1141 removed outlier: 4.758A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D1140 " --> pdb=" O LEU D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1149 No H-bonds generated for 'chain 'D' and resid 1147 through 1149' Processing helix chain 'D' and resid 1150 through 1163 removed outlier: 4.116A pdb=" N SER D1154 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D1158 " --> pdb=" O SER D1154 " (cutoff:3.500A) removed outlier: 3.649A 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 1239 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 267 through 275 removed outlier: 6.566A pdb=" N PHE A 141 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 143 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 140 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU A 184 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 221 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 364 " --> pdb=" O ILE A 338 " (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 221 through 222 removed outlier: 6.315A pdb=" N THR B 222 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 219 removed outlier: 3.541A pdb=" N VAL B 335 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 339 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'C' and resid 267 through 275 removed outlier: 6.853A pdb=" N PHE C 141 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL C 270 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR C 143 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 140 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 186 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE C 221 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 339 " --> pdb=" O HIS C 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'D' and resid 268 through 275 removed outlier: 6.616A pdb=" N PHE D 141 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL D 270 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 143 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) 1787 hydrogen bonds defined for protein. 5274 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: 6.58 Time building geometry restraints manager: 3.75 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: 13028 1.47 - 1.69: 14432 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 0.834 0.700 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 0.834 0.700 2.00e-02 2.50e+03 1.22e+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=" C03 9Z9 C1402 " pdb=" C74 9Z9 C1402 " ideal model delta sigma weight residual 1.534 0.835 0.699 2.00e-02 2.50e+03 1.22e+03 bond pdb=" C02 9Z9 A1402 " pdb=" C03 9Z9 A1402 " 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 - 10.32: 44556 10.32 - 20.63: 12 20.63 - 30.95: 8 30.95 - 41.27: 4 41.27 - 51.59: 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 114.05 165.64 -51.59 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 114.05 165.63 -51.58 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C74 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" C76 9Z9 C1402 " ideal model delta sigma weight residual 114.05 165.62 -51.57 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C74 9Z9 B1402 " pdb=" C73 9Z9 B1402 " pdb=" C76 9Z9 B1402 " ideal model delta sigma weight residual 114.05 165.60 -51.55 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C76 9Z9 C1402 " pdb=" C73 9Z9 C1402 " pdb=" O72 9Z9 C1402 " ideal model delta sigma weight residual 109.02 70.26 38.76 3.00e+00 1.11e-01 1.67e+02 ... (remaining 44579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 18848 24.76 - 49.51: 710 49.51 - 74.27: 84 74.27 - 99.02: 9 99.02 - 123.78: 4 Dihedral angle restraints: 19655 sinusoidal: 8163 harmonic: 11492 Sorted by residual: dihedral pdb=" CA THR B 356 " pdb=" C THR B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+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 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 9.58e+01 chirality pdb=" C03 9Z9 C1402 " pdb=" C02 9Z9 C1402 " pdb=" C04 9Z9 C1402 " pdb=" C74 9Z9 C1402 " both_signs ideal model delta sigma weight residual False 2.78 0.82 1.96 2.00e-01 2.50e+01 9.58e+01 ... (remaining 4977 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 784 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO B 785 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 785 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A 785 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " -0.038 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C 785 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " -0.032 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3864 2.75 - 3.29: 31742 3.29 - 3.82: 51141 3.82 - 4.36: 58072 4.36 - 4.90: 103670 Nonbonded interactions: 248489 Sorted by model distance: nonbonded pdb=" OG SER A 187 " pdb=" OE2 GLU A 316 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU B 524 " pdb=" OH TYR B 585 " model vdw 2.222 3.040 nonbonded pdb=" OG SER D 556 " pdb=" OD1 ASP D 559 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU D 524 " pdb=" OH TYR D 585 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.249 3.040 ... (remaining 248484 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' selection = (chain 'B' and resid 129 through 1403) 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.200 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 0.700 32968 Z= 0.769 Angle : 1.044 51.585 44584 Z= 0.426 Chirality : 0.076 1.959 4980 Planarity : 0.004 0.057 5516 Dihedral : 12.520 123.777 12223 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.12 % Rotamer: Outliers : 2.91 % Allowed : 6.03 % Favored : 91.06 % 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: 0.04 (0.14), residues: 3824 helix: 0.92 (0.11), residues: 2420 sheet: -0.88 (0.33), residues: 264 loop : -1.62 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.013 0.001 TYR D1048 PHE 0.010 0.001 PHE C 205 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 0.01526 / 0.77 (32968) covalent geometry : angle 1.04441 / 0.43 (44584) hydrogen bonds : bond 0.15807 / 10.65 ( 1787) hydrogen bonds : angle 5.43576 / 3.84 ( 5274) *********************** 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 620 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 520 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.6940 (ppp) cc_final: 0.6383 (mmp) REVERT: A 923 ILE cc_start: 0.8464 (tt) cc_final: 0.8225 (tt) REVERT: A 958 MET cc_start: 0.7704 (tmm) cc_final: 0.7423 (ttp) REVERT: A 1013 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (t80) REVERT: B 317 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8313 (mmmt) REVERT: B 923 ILE cc_start: 0.8456 (tt) cc_final: 0.8197 (tt) REVERT: B 958 MET cc_start: 0.7609 (tmm) cc_final: 0.7265 (ttp) REVERT: B 1011 MET cc_start: 0.7265 (mmt) cc_final: 0.6966 (mmt) REVERT: B 1013 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8637 (t80) REVERT: C 778 ILE cc_start: 0.8414 (mm) cc_final: 0.8128 (mm) REVERT: C 923 ILE cc_start: 0.8492 (tt) cc_final: 0.8217 (tt) REVERT: C 958 MET cc_start: 0.7702 (tmm) cc_final: 0.7327 (ttp) REVERT: D 281 MET cc_start: 0.6768 (ppp) cc_final: 0.5974 (mmp) REVERT: D 778 ILE cc_start: 0.8344 (mm) cc_final: 0.8125 (mm) REVERT: D 923 ILE cc_start: 0.8464 (tt) cc_final: 0.8232 (tt) REVERT: D 958 MET cc_start: 0.7569 (tmm) cc_final: 0.7269 (ttp) REVERT: D 1017 MET cc_start: 0.6158 (mtt) cc_final: 0.5832 (mtt) REVERT: D 1185 ILE cc_start: 0.7074 (pt) cc_final: 0.6802 (pt) outliers start: 100 outliers final: 28 residues processed: 601 average time/residue: 0.1876 time to fit residues: 185.8715 Evaluate side-chains 407 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 586 HIS A 659 GLN A 697 HIS A 746 HIS A 940 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1115 ASN A1116 ASN A1161 GLN A1238 ASN B 178 GLN B 291 HIS B 314 GLN B 378 HIS B 411 GLN B 586 HIS B 659 GLN B 697 HIS B 746 HIS B 940 GLN B 978 ASN B1115 ASN B1116 ASN B1161 GLN C 151 HIS C 178 GLN C 194 ASN C 586 HIS C 659 GLN C 697 HIS C 746 HIS C 940 GLN C 944 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 ASN C1115 ASN C1116 ASN C1161 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 586 HIS D 659 GLN D 697 HIS D 746 HIS D 940 GLN D 978 ASN D 993 ASN D1115 ASN D1116 ASN D1161 GLN D1238 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107041 restraints weight = 46253.344| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.63 r_work: 0.3132 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32968 Z= 0.177 Angle : 0.594 7.979 44584 Z= 0.296 Chirality : 0.040 0.183 4980 Planarity : 0.004 0.044 5516 Dihedral : 9.107 117.548 4551 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.53 % Allowed : 10.51 % Favored : 86.96 % 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: 0.44 (0.14), residues: 3824 helix: 1.38 (0.11), residues: 2436 sheet: -1.09 (0.31), residues: 264 loop : -1.79 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 768 TYR 0.013 0.001 TYR B 865 PHE 0.016 0.001 PHE B 877 TRP 0.014 0.001 TRP D 763 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (32968) covalent geometry : angle 0.59362 / 0.30 (44584) hydrogen bonds : bond 0.05135 / 3.51 ( 1787) hydrogen bonds : angle 4.04075 / 2.86 ( 5274) *********************** 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 506 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 419 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7915 (tt0) REVERT: A 168 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 281 MET cc_start: 0.7412 (ppp) cc_final: 0.6662 (mmt) REVERT: A 421 MET cc_start: 0.8436 (mmp) cc_final: 0.8168 (mmp) REVERT: A 892 ILE cc_start: 0.8698 (tp) cc_final: 0.8489 (pt) REVERT: A 1013 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8775 (t80) REVERT: B 145 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7931 (tt0) REVERT: B 162 PHE cc_start: 0.6268 (p90) cc_final: 0.6019 (p90) REVERT: B 171 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8049 (t-90) REVERT: B 397 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7421 (p) REVERT: B 767 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8090 (mt) REVERT: B 892 ILE cc_start: 0.8554 (tp) cc_final: 0.8290 (pt) REVERT: B 1013 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8857 (t80) REVERT: B 1053 MET cc_start: 0.8532 (ttm) cc_final: 0.8276 (ttt) REVERT: B 1095 MET cc_start: 0.7681 (ttp) cc_final: 0.7474 (ttp) REVERT: B 1206 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7872 (ttp-170) REVERT: C 145 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7960 (tt0) REVERT: C 168 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8500 (mm) REVERT: C 281 MET cc_start: 0.7227 (mmt) cc_final: 0.6295 (ptt) REVERT: C 421 MET cc_start: 0.8424 (mmp) cc_final: 0.8182 (mmp) REVERT: C 687 MET cc_start: 0.6689 (mmp) cc_final: 0.6055 (tpp) REVERT: C 892 ILE cc_start: 0.8694 (tp) cc_final: 0.8483 (pt) REVERT: D 168 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8486 (mm) REVERT: D 239 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7821 (t0) REVERT: D 281 MET cc_start: 0.7185 (ppp) cc_final: 0.6265 (mmp) REVERT: D 687 MET cc_start: 0.6988 (mmm) cc_final: 0.6494 (mmt) REVERT: D 767 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8222 (mt) REVERT: D 892 ILE cc_start: 0.8531 (tp) cc_final: 0.8277 (pt) REVERT: D 1017 MET cc_start: 0.6820 (mtt) cc_final: 0.6346 (mtt) REVERT: D 1142 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8095 (tp30) outliers start: 87 outliers final: 44 residues processed: 479 average time/residue: 0.1859 time to fit residues: 150.2173 Evaluate side-chains 428 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 332 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 453 ASN A 746 HIS A 890 ASN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 409 GLN B 746 HIS B 944 ASN B1115 ASN C 151 HIS C 746 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 869 ASN D1115 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106678 restraints weight = 46787.609| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.68 r_work: 0.3129 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32968 Z= 0.157 Angle : 0.554 8.461 44584 Z= 0.276 Chirality : 0.038 0.165 4980 Planarity : 0.004 0.043 5516 Dihedral : 8.711 112.405 4532 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.94 % Allowed : 11.27 % Favored : 85.79 % 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: 0.66 (0.14), residues: 3824 helix: 1.59 (0.11), residues: 2432 sheet: -1.24 (0.31), residues: 264 loop : -1.72 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 768 TYR 0.020 0.001 TYR D 865 PHE 0.015 0.001 PHE A 877 TRP 0.014 0.001 TRP D 763 HIS 0.015 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (32968) covalent geometry : angle 0.55448 / 0.28 (44584) hydrogen bonds : bond 0.04818 / 3.29 ( 1787) hydrogen bonds : angle 3.83518 / 2.70 ( 5274) *********************** 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 507 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 406 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7941 (tt0) REVERT: A 168 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 245 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7221 (mpt180) REVERT: A 262 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: A 281 MET cc_start: 0.7482 (ppp) cc_final: 0.6728 (mmt) REVERT: A 369 ARG cc_start: 0.6882 (tpp80) cc_final: 0.6521 (tpp80) REVERT: A 418 MET cc_start: 0.5155 (tpt) cc_final: 0.4752 (ttm) REVERT: A 482 GLN cc_start: 0.8543 (tt0) cc_final: 0.8044 (tm-30) REVERT: A 769 MET cc_start: 0.6063 (mtt) cc_final: 0.5789 (mtt) REVERT: A 892 ILE cc_start: 0.8694 (tp) cc_final: 0.8383 (pt) REVERT: A 1013 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8788 (t80) REVERT: B 145 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7862 (tt0) REVERT: B 162 PHE cc_start: 0.6288 (p90) cc_final: 0.6012 (p90) REVERT: B 171 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8003 (t-90) REVERT: B 279 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5845 (p0) REVERT: B 397 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7470 (p) REVERT: B 409 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: B 769 MET cc_start: 0.7871 (mpp) cc_final: 0.7148 (mpt) REVERT: B 892 ILE cc_start: 0.8503 (tp) cc_final: 0.8214 (pt) REVERT: B 1013 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 1053 MET cc_start: 0.8630 (ttm) cc_final: 0.8395 (ttt) REVERT: B 1095 MET cc_start: 0.7648 (ttp) cc_final: 0.7438 (ttp) REVERT: B 1232 MET cc_start: 0.7847 (tmm) cc_final: 0.7605 (tmm) REVERT: C 145 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7926 (tt0) REVERT: C 151 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7045 (p-80) REVERT: C 168 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8471 (mm) REVERT: C 281 MET cc_start: 0.7290 (mmt) cc_final: 0.6437 (ptt) REVERT: C 687 MET cc_start: 0.6776 (mmp) cc_final: 0.6182 (tpp) REVERT: C 769 MET cc_start: 0.6656 (mtt) cc_final: 0.6451 (mtm) REVERT: C 892 ILE cc_start: 0.8640 (tp) cc_final: 0.8352 (pt) REVERT: D 168 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8492 (mm) REVERT: D 239 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7857 (t0) REVERT: D 281 MET cc_start: 0.7252 (ppp) cc_final: 0.6261 (mmp) REVERT: D 687 MET cc_start: 0.6995 (mmm) cc_final: 0.6734 (tpp) REVERT: D 767 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8186 (mt) REVERT: D 892 ILE cc_start: 0.8515 (tp) cc_final: 0.8212 (pt) REVERT: D 1017 MET cc_start: 0.6803 (mtt) cc_final: 0.6337 (mtt) outliers start: 101 outliers final: 55 residues processed: 481 average time/residue: 0.1833 time to fit residues: 148.6836 Evaluate side-chains 450 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 746 HIS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 746 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1002 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 214 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 67 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 ASN A 746 HIS A 978 ASN A1115 ASN A1155 HIS B 453 ASN B 586 HIS B 746 HIS B 890 ASN B1141 HIS C 151 HIS C 746 HIS C 890 ASN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 890 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108431 restraints weight = 46459.826| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.68 r_work: 0.3152 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32968 Z= 0.118 Angle : 0.518 7.978 44584 Z= 0.257 Chirality : 0.037 0.153 4980 Planarity : 0.004 0.042 5516 Dihedral : 8.451 106.834 4529 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 2.68 % Allowed : 12.52 % Favored : 84.80 % 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: 0.85 (0.14), residues: 3824 helix: 1.77 (0.11), residues: 2436 sheet: -1.23 (0.31), residues: 264 loop : -1.72 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 231 TYR 0.032 0.001 TYR D 380 PHE 0.018 0.001 PHE C1047 TRP 0.012 0.001 TRP C 763 HIS 0.004 0.000 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (32968) covalent geometry : angle 0.51776 / 0.26 (44584) hydrogen bonds : bond 0.04303 / 2.94 ( 1787) hydrogen bonds : angle 3.66484 / 2.57 ( 5274) *********************** 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 498 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 406 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7903 (tt0) REVERT: A 168 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 245 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7388 (mpt180) REVERT: A 262 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: A 281 MET cc_start: 0.7522 (ppp) cc_final: 0.6781 (mmt) REVERT: A 369 ARG cc_start: 0.6847 (tpp80) cc_final: 0.6646 (tpp80) REVERT: A 418 MET cc_start: 0.5176 (tpt) cc_final: 0.4766 (ttm) REVERT: A 421 MET cc_start: 0.8061 (mmp) cc_final: 0.7753 (mmm) REVERT: A 482 GLN cc_start: 0.8501 (tt0) cc_final: 0.8019 (tm-30) REVERT: A 892 ILE cc_start: 0.8627 (tp) cc_final: 0.8365 (pt) REVERT: A 1013 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8835 (t80) REVERT: B 145 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7867 (tt0) REVERT: B 162 PHE cc_start: 0.6321 (p90) cc_final: 0.6079 (p90) REVERT: B 171 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8036 (t-90) REVERT: B 245 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7672 (mpt180) REVERT: B 397 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7475 (p) REVERT: B 769 MET cc_start: 0.7836 (mpp) cc_final: 0.7089 (mpt) REVERT: B 892 ILE cc_start: 0.8526 (tp) cc_final: 0.8245 (pt) REVERT: B 941 GLU cc_start: 0.8154 (mp0) cc_final: 0.7904 (mp0) REVERT: B 1013 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8768 (t80) REVERT: B 1142 GLU cc_start: 0.8740 (tp30) cc_final: 0.8241 (mt-10) REVERT: B 1232 MET cc_start: 0.7842 (tmm) cc_final: 0.7595 (tmm) REVERT: C 145 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7889 (tt0) REVERT: C 151 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7216 (p-80) REVERT: C 168 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8470 (mm) REVERT: C 281 MET cc_start: 0.7343 (mmt) cc_final: 0.6516 (ptt) REVERT: C 687 MET cc_start: 0.6767 (mmp) cc_final: 0.6211 (tpp) REVERT: C 892 ILE cc_start: 0.8475 (tp) cc_final: 0.8161 (pt) REVERT: D 168 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8469 (mm) REVERT: D 239 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7885 (t0) REVERT: D 281 MET cc_start: 0.7266 (ppp) cc_final: 0.6259 (mmp) REVERT: D 687 MET cc_start: 0.7043 (mmm) cc_final: 0.6808 (tpp) REVERT: D 767 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8098 (mt) REVERT: D 892 ILE cc_start: 0.8497 (tp) cc_final: 0.8211 (pt) REVERT: D 1017 MET cc_start: 0.6742 (mtt) cc_final: 0.6276 (mtt) REVERT: D 1142 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8038 (tp30) outliers start: 92 outliers final: 58 residues processed: 475 average time/residue: 0.1870 time to fit residues: 150.1850 Evaluate side-chains 448 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 379 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1002 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 115 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 375 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN B 586 HIS ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104990 restraints weight = 46669.301| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.65 r_work: 0.3102 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32968 Z= 0.205 Angle : 0.581 8.455 44584 Z= 0.288 Chirality : 0.040 0.193 4980 Planarity : 0.004 0.043 5516 Dihedral : 8.435 100.954 4529 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 3.26 % Allowed : 12.98 % Favored : 83.76 % 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: 0.80 (0.14), residues: 3824 helix: 1.71 (0.11), residues: 2432 sheet: -1.39 (0.31), residues: 252 loop : -1.66 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.033 0.001 TYR D 380 PHE 0.028 0.001 PHE C1047 TRP 0.016 0.001 TRP C 763 HIS 0.011 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.20 (32968) covalent geometry : angle 0.58087 / 0.29 (44584) hydrogen bonds : bond 0.04993 / 3.41 ( 1787) hydrogen bonds : angle 3.76455 / 2.65 ( 5274) *********************** 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 504 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 392 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7880 (tt0) REVERT: A 168 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 245 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7458 (mpt180) REVERT: A 262 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: A 281 MET cc_start: 0.7543 (ppp) cc_final: 0.6745 (mmt) REVERT: A 369 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6673 (tpp80) REVERT: A 421 MET cc_start: 0.8181 (mmp) cc_final: 0.7845 (mmm) REVERT: A 482 GLN cc_start: 0.8460 (tt0) cc_final: 0.8142 (tm-30) REVERT: A 892 ILE cc_start: 0.8651 (tp) cc_final: 0.8347 (pt) REVERT: A 1013 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8768 (t80) REVERT: A 1017 MET cc_start: 0.7109 (mtm) cc_final: 0.6666 (mtt) REVERT: B 145 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7862 (tt0) REVERT: B 171 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8084 (t-90) REVERT: B 264 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (p0) REVERT: B 265 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7348 (mp) REVERT: B 279 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.5776 (p0) REVERT: B 397 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7526 (p) REVERT: B 769 MET cc_start: 0.7914 (mpp) cc_final: 0.7066 (mpp) REVERT: B 892 ILE cc_start: 0.8551 (tp) cc_final: 0.8207 (pt) REVERT: B 1013 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8810 (t80) REVERT: B 1017 MET cc_start: 0.7150 (mtm) cc_final: 0.6937 (mtm) REVERT: C 145 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7862 (tt0) REVERT: C 168 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (mm) REVERT: C 281 MET cc_start: 0.7390 (mmt) cc_final: 0.6591 (ptt) REVERT: C 687 MET cc_start: 0.7112 (mmp) cc_final: 0.6572 (tpp) REVERT: C 892 ILE cc_start: 0.8622 (tp) cc_final: 0.8284 (pt) REVERT: D 168 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8500 (mm) REVERT: D 239 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7942 (t0) REVERT: D 281 MET cc_start: 0.7294 (ppp) cc_final: 0.6275 (mmp) REVERT: D 687 MET cc_start: 0.7149 (mmm) cc_final: 0.6931 (tpp) REVERT: D 767 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8146 (mt) REVERT: D 892 ILE cc_start: 0.8545 (tp) cc_final: 0.8234 (pt) REVERT: D 1017 MET cc_start: 0.6816 (mtt) cc_final: 0.6324 (mtt) outliers start: 112 outliers final: 74 residues processed: 472 average time/residue: 0.1872 time to fit residues: 150.0183 Evaluate side-chains 464 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 377 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 731 ASN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 731 ASN Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1002 MET Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.0870 chunk 233 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 67 optimal weight: 0.0000 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 453 ASN B 586 HIS ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108114 restraints weight = 46366.896| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.67 r_work: 0.3149 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32968 Z= 0.114 Angle : 0.517 8.626 44584 Z= 0.256 Chirality : 0.037 0.189 4980 Planarity : 0.003 0.040 5516 Dihedral : 8.159 93.085 4529 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 2.94 % Allowed : 13.80 % Favored : 83.26 % 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: 1.91 (0.11), residues: 2436 sheet: -1.01 (0.34), residues: 208 loop : -1.66 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 231 TYR 0.037 0.001 TYR D 380 PHE 0.027 0.001 PHE A1047 TRP 0.013 0.001 TRP C 763 HIS 0.002 0.000 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (32968) covalent geometry : angle 0.51730 / 0.26 (44584) hydrogen bonds : bond 0.04190 / 2.86 ( 1787) hydrogen bonds : angle 3.59511 / 2.52 ( 5274) *********************** 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 504 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 403 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7889 (tt0) REVERT: A 168 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 245 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7421 (mpt180) REVERT: A 262 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: A 281 MET cc_start: 0.7542 (ppp) cc_final: 0.6745 (mmt) REVERT: A 369 ARG cc_start: 0.7032 (tpp80) cc_final: 0.6686 (tpp80) REVERT: A 418 MET cc_start: 0.5132 (tpt) cc_final: 0.4716 (ttm) REVERT: A 421 MET cc_start: 0.8353 (mmp) cc_final: 0.8071 (mmm) REVERT: A 496 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8846 (mp) REVERT: A 892 ILE cc_start: 0.8457 (tp) cc_final: 0.8130 (pt) REVERT: A 1013 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8820 (t80) REVERT: B 145 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7833 (tt0) REVERT: B 171 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: B 245 ARG cc_start: 0.7887 (mpt180) cc_final: 0.7605 (mpt180) REVERT: B 264 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7624 (p0) REVERT: B 265 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7214 (mp) REVERT: B 397 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 769 MET cc_start: 0.7853 (mpp) cc_final: 0.7129 (mpp) REVERT: B 892 ILE cc_start: 0.8591 (tp) cc_final: 0.8233 (pt) REVERT: B 1013 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8747 (t80) REVERT: B 1142 GLU cc_start: 0.8685 (tp30) cc_final: 0.8198 (tt0) REVERT: C 145 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7837 (tt0) REVERT: C 151 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6987 (p-80) REVERT: C 168 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8443 (mm) REVERT: C 245 ARG cc_start: 0.7536 (mmt90) cc_final: 0.7229 (mmt-90) REVERT: C 281 MET cc_start: 0.7343 (mmt) cc_final: 0.6671 (ptm) REVERT: C 687 MET cc_start: 0.7212 (mmp) cc_final: 0.6714 (tpp) REVERT: C 769 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6817 (mpp) REVERT: C 892 ILE cc_start: 0.8446 (tp) cc_final: 0.8093 (pt) REVERT: D 168 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (mm) REVERT: D 239 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7954 (t0) REVERT: D 258 ILE cc_start: 0.7946 (mm) cc_final: 0.7745 (tp) REVERT: D 281 MET cc_start: 0.7209 (ppp) cc_final: 0.6193 (mmp) REVERT: D 892 ILE cc_start: 0.8531 (tp) cc_final: 0.8177 (pt) REVERT: D 1017 MET cc_start: 0.6735 (mtt) cc_final: 0.6261 (mtt) REVERT: D 1142 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8076 (tp30) outliers start: 101 outliers final: 60 residues processed: 475 average time/residue: 0.1876 time to fit residues: 150.7279 Evaluate side-chains 460 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 386 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 586 HIS ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103499 restraints weight = 47233.978| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.67 r_work: 0.3081 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 32968 Z= 0.244 Angle : 0.617 9.427 44584 Z= 0.306 Chirality : 0.041 0.188 4980 Planarity : 0.004 0.045 5516 Dihedral : 8.245 86.488 4527 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.04 % Rotamer: Outliers : 3.17 % Allowed : 13.92 % Favored : 82.91 % 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: 0.80 (0.14), residues: 3824 helix: 1.73 (0.11), residues: 2436 sheet: -1.50 (0.30), residues: 252 loop : -1.67 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.037 0.002 TYR D 380 PHE 0.031 0.002 PHE A1047 TRP 0.017 0.002 TRP D 763 HIS 0.017 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.24 (32968) covalent geometry : angle 0.61704 / 0.31 (44584) hydrogen bonds : bond 0.05257 / 3.58 ( 1787) hydrogen bonds : angle 3.79845 / 2.67 ( 5274) *********************** 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 499 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 390 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7892 (tt0) REVERT: A 168 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 245 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7463 (mpt180) REVERT: A 281 MET cc_start: 0.7647 (ppp) cc_final: 0.6724 (mmt) REVERT: A 421 MET cc_start: 0.8295 (mmp) cc_final: 0.8010 (mmm) REVERT: A 492 MET cc_start: 0.8851 (tpp) cc_final: 0.8436 (tpt) REVERT: A 496 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 892 ILE cc_start: 0.8619 (tp) cc_final: 0.8366 (pt) REVERT: A 1017 MET cc_start: 0.7026 (mtm) cc_final: 0.6665 (mtm) REVERT: B 145 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7891 (tt0) REVERT: B 170 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8443 (tt) REVERT: B 264 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7624 (p0) REVERT: B 265 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7352 (mp) REVERT: B 279 ASN cc_start: 0.6296 (OUTLIER) cc_final: 0.5609 (p0) REVERT: B 397 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7715 (p) REVERT: B 769 MET cc_start: 0.7944 (mpp) cc_final: 0.7273 (mpp) REVERT: B 892 ILE cc_start: 0.8536 (tp) cc_final: 0.8199 (pt) REVERT: B 1017 MET cc_start: 0.7108 (mtm) cc_final: 0.6667 (mtt) REVERT: B 1142 GLU cc_start: 0.8757 (tp30) cc_final: 0.8291 (tt0) REVERT: C 145 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7854 (tt0) REVERT: C 151 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6863 (p90) REVERT: C 168 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8489 (mm) REVERT: C 281 MET cc_start: 0.7333 (mmt) cc_final: 0.6775 (ptt) REVERT: C 687 MET cc_start: 0.7350 (mmp) cc_final: 0.6857 (tpp) REVERT: C 892 ILE cc_start: 0.8592 (tp) cc_final: 0.8360 (pt) REVERT: C 1017 MET cc_start: 0.6984 (mtm) cc_final: 0.6698 (mtt) REVERT: D 168 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8504 (mm) REVERT: D 239 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8021 (t0) REVERT: D 281 MET cc_start: 0.7305 (ppp) cc_final: 0.6171 (mmp) REVERT: D 421 MET cc_start: 0.8436 (mmm) cc_final: 0.7811 (mmm) REVERT: D 687 MET cc_start: 0.7229 (tpp) cc_final: 0.6844 (mmp) REVERT: D 892 ILE cc_start: 0.8465 (tp) cc_final: 0.8222 (pt) REVERT: D 1017 MET cc_start: 0.6848 (mtt) cc_final: 0.6351 (mtt) REVERT: D 1061 ASP cc_start: 0.8461 (m-30) cc_final: 0.7885 (t70) outliers start: 109 outliers final: 72 residues processed: 471 average time/residue: 0.1855 time to fit residues: 148.0324 Evaluate side-chains 464 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 381 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 731 ASN Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 731 ASN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1063 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: 0.7980 chunk 31 optimal weight: 1.9990 chunk 331 optimal weight: 0.0970 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN B 409 GLN B 453 ASN B1115 ASN C 151 HIS C 586 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN D 586 HIS D1115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107064 restraints weight = 46613.003| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.67 r_work: 0.3134 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32968 Z= 0.126 Angle : 0.539 10.757 44584 Z= 0.266 Chirality : 0.038 0.189 4980 Planarity : 0.003 0.041 5516 Dihedral : 8.022 79.490 4525 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 2.85 % Allowed : 14.44 % Favored : 82.71 % 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: 1.92 (0.11), residues: 2432 sheet: -1.04 (0.33), residues: 208 loop : -1.63 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.040 0.001 TYR D 380 PHE 0.028 0.001 PHE C1047 TRP 0.014 0.001 TRP C 763 HIS 0.016 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (32968) covalent geometry : angle 0.53920 / 0.27 (44584) hydrogen bonds : bond 0.04414 / 3.01 ( 1787) hydrogen bonds : angle 3.61829 / 2.54 ( 5274) *********************** 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 493 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 395 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7881 (tt0) REVERT: A 151 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6834 (p90) REVERT: A 168 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 245 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7444 (mpt180) REVERT: A 281 MET cc_start: 0.7627 (ppp) cc_final: 0.6718 (mmp) REVERT: A 369 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6745 (tpp80) REVERT: A 421 MET cc_start: 0.8393 (mmp) cc_final: 0.8083 (mmm) REVERT: A 492 MET cc_start: 0.8765 (tpp) cc_final: 0.8462 (tpt) REVERT: A 496 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 514 MET cc_start: 0.8664 (tpp) cc_final: 0.8415 (mmp) REVERT: A 892 ILE cc_start: 0.8455 (tp) cc_final: 0.8105 (pt) REVERT: A 1013 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8751 (t80) REVERT: A 1017 MET cc_start: 0.6954 (mtm) cc_final: 0.6512 (mtt) REVERT: B 145 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7853 (tt0) REVERT: B 170 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 171 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8019 (t-90) REVERT: B 264 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7736 (p0) REVERT: B 265 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7272 (mp) REVERT: B 397 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7694 (p) REVERT: B 409 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: B 769 MET cc_start: 0.7833 (mpp) cc_final: 0.7197 (mpp) REVERT: B 892 ILE cc_start: 0.8564 (tp) cc_final: 0.8202 (pt) REVERT: B 1013 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8770 (t80) REVERT: B 1017 MET cc_start: 0.7038 (mtm) cc_final: 0.6551 (mtt) REVERT: B 1142 GLU cc_start: 0.8736 (tp30) cc_final: 0.8295 (tt0) REVERT: C 145 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7861 (tt0) REVERT: C 151 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7149 (p-80) REVERT: C 168 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 245 ARG cc_start: 0.7580 (mmt90) cc_final: 0.7224 (mmt-90) REVERT: C 281 MET cc_start: 0.7282 (mmt) cc_final: 0.6765 (ptt) REVERT: C 687 MET cc_start: 0.7348 (mmp) cc_final: 0.6869 (tpp) REVERT: C 769 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6934 (mpp) REVERT: C 892 ILE cc_start: 0.8445 (tp) cc_final: 0.8068 (pt) REVERT: D 168 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8477 (mm) REVERT: D 239 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8003 (t0) REVERT: D 281 MET cc_start: 0.7212 (ppp) cc_final: 0.6155 (mmp) REVERT: D 421 MET cc_start: 0.8314 (mmm) cc_final: 0.7798 (mmm) REVERT: D 687 MET cc_start: 0.7128 (tpp) cc_final: 0.6769 (mmp) REVERT: D 892 ILE cc_start: 0.8473 (tp) cc_final: 0.8121 (pt) REVERT: D 1017 MET cc_start: 0.6750 (mtt) cc_final: 0.6272 (mtt) REVERT: D 1142 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8112 (tp30) outliers start: 98 outliers final: 68 residues processed: 468 average time/residue: 0.1909 time to fit residues: 150.5760 Evaluate side-chains 469 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 385 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 769 MET Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 30 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 224 optimal weight: 0.3980 chunk 339 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 259 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 453 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 586 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106663 restraints weight = 46399.493| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.67 r_work: 0.3128 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32968 Z= 0.144 Angle : 0.551 11.232 44584 Z= 0.271 Chirality : 0.038 0.185 4980 Planarity : 0.004 0.042 5516 Dihedral : 7.936 73.585 4525 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 2.71 % Allowed : 14.38 % Favored : 82.91 % 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: 1.94 (0.11), residues: 2432 sheet: -1.42 (0.30), residues: 252 loop : -1.61 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 407 TYR 0.038 0.001 TYR D 380 PHE 0.029 0.001 PHE A1047 TRP 0.014 0.001 TRP C 763 HIS 0.010 0.000 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (32968) covalent geometry : angle 0.55112 / 0.27 (44584) hydrogen bonds : bond 0.04448 / 3.04 ( 1787) hydrogen bonds : angle 3.61078 / 2.54 ( 5274) *********************** 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 485 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7879 (tt0) REVERT: A 151 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6879 (p-80) REVERT: A 168 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 245 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7414 (mpt180) REVERT: A 281 MET cc_start: 0.7633 (ppp) cc_final: 0.6720 (mmp) REVERT: A 369 ARG cc_start: 0.7149 (tpp80) cc_final: 0.6836 (tpp80) REVERT: A 421 MET cc_start: 0.8399 (mmp) cc_final: 0.8068 (mmm) REVERT: A 496 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 514 MET cc_start: 0.8687 (tpp) cc_final: 0.8460 (mmp) REVERT: A 892 ILE cc_start: 0.8499 (tp) cc_final: 0.8156 (pt) REVERT: A 1013 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.8770 (t80) REVERT: B 145 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7845 (tt0) REVERT: B 170 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 171 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8026 (t-90) REVERT: B 264 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7686 (p0) REVERT: B 265 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7345 (mp) REVERT: B 397 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7659 (p) REVERT: B 409 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: B 769 MET cc_start: 0.7866 (mpp) cc_final: 0.7240 (mpp) REVERT: B 892 ILE cc_start: 0.8513 (tp) cc_final: 0.8148 (pt) REVERT: B 1013 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8691 (t80) REVERT: B 1017 MET cc_start: 0.7041 (mtm) cc_final: 0.6561 (mtt) REVERT: B 1142 GLU cc_start: 0.8728 (tp30) cc_final: 0.8314 (tt0) REVERT: C 145 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7852 (tt0) REVERT: C 151 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6827 (p-80) REVERT: C 168 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8465 (mm) REVERT: C 245 ARG cc_start: 0.7575 (mmt90) cc_final: 0.7254 (mmt-90) REVERT: C 281 MET cc_start: 0.7273 (mmt) cc_final: 0.6760 (ptt) REVERT: C 514 MET cc_start: 0.8845 (mmm) cc_final: 0.8476 (mmp) REVERT: C 687 MET cc_start: 0.7363 (mmp) cc_final: 0.6882 (tpp) REVERT: C 892 ILE cc_start: 0.8477 (tp) cc_final: 0.8110 (pt) REVERT: D 168 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8481 (mm) REVERT: D 239 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7987 (t0) REVERT: D 281 MET cc_start: 0.7228 (ppp) cc_final: 0.6096 (mmp) REVERT: D 687 MET cc_start: 0.7167 (tpp) cc_final: 0.6819 (mmp) REVERT: D 892 ILE cc_start: 0.8531 (tp) cc_final: 0.8187 (pt) REVERT: D 1017 MET cc_start: 0.6780 (mtt) cc_final: 0.6287 (mtt) REVERT: D 1142 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8111 (tp30) outliers start: 93 outliers final: 67 residues processed: 461 average time/residue: 0.1883 time to fit residues: 146.0688 Evaluate side-chains 468 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 386 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1185 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1002 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 Chi-restraints excluded: chain D residue 1227 VAL 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: 4.9990 chunk 245 optimal weight: 1.9990 chunk 179 optimal weight: 0.0040 chunk 203 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 358 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 586 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106049 restraints weight = 46908.189| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.68 r_work: 0.3117 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32968 Z= 0.161 Angle : 0.562 11.374 44584 Z= 0.276 Chirality : 0.039 0.189 4980 Planarity : 0.004 0.042 5516 Dihedral : 7.918 67.694 4525 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 2.50 % Allowed : 14.59 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3824 helix: 1.92 (0.11), residues: 2432 sheet: -1.46 (0.30), residues: 264 loop : -1.66 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 354 TYR 0.037 0.001 TYR D 380 PHE 0.030 0.001 PHE A1047 TRP 0.014 0.001 TRP D 763 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (32968) covalent geometry : angle 0.56156 / 0.28 (44584) hydrogen bonds : bond 0.04571 / 3.12 ( 1787) hydrogen bonds : angle 3.62714 / 2.55 ( 5274) ********************** 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 477 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 391 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7898 (tt0) REVERT: A 151 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6953 (p90) REVERT: A 168 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 245 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7394 (mpt180) REVERT: A 281 MET cc_start: 0.7647 (ppp) cc_final: 0.6756 (mmp) REVERT: A 369 ARG cc_start: 0.7136 (tpp80) cc_final: 0.6822 (tpp80) REVERT: A 421 MET cc_start: 0.8328 (mmp) cc_final: 0.8005 (mmm) REVERT: A 496 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8830 (mp) REVERT: A 892 ILE cc_start: 0.8504 (tp) cc_final: 0.8153 (pt) REVERT: A 1013 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8777 (t80) REVERT: A 1017 MET cc_start: 0.7005 (mtm) cc_final: 0.6575 (mtt) REVERT: B 145 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7859 (tt0) REVERT: B 170 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 171 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8007 (t-90) REVERT: B 264 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7713 (p0) REVERT: B 265 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 397 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7678 (p) REVERT: B 769 MET cc_start: 0.7867 (mpp) cc_final: 0.7227 (mpp) REVERT: B 892 ILE cc_start: 0.8548 (tp) cc_final: 0.8184 (pt) REVERT: B 1013 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8694 (t80) REVERT: B 1017 MET cc_start: 0.7060 (mtm) cc_final: 0.6592 (mtt) REVERT: B 1142 GLU cc_start: 0.8742 (tp30) cc_final: 0.8339 (tt0) REVERT: C 145 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7857 (tt0) REVERT: C 151 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6797 (p-80) REVERT: C 168 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 245 ARG cc_start: 0.7608 (mmt90) cc_final: 0.7284 (mmt-90) REVERT: C 281 MET cc_start: 0.7243 (mmt) cc_final: 0.6629 (ptt) REVERT: C 514 MET cc_start: 0.8837 (mmm) cc_final: 0.8559 (mmp) REVERT: C 687 MET cc_start: 0.7393 (mmp) cc_final: 0.6910 (tpp) REVERT: C 892 ILE cc_start: 0.8467 (tp) cc_final: 0.8090 (pt) REVERT: C 1017 MET cc_start: 0.6896 (mtm) cc_final: 0.6628 (mtt) REVERT: D 168 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8486 (mm) REVERT: D 239 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8010 (t0) REVERT: D 482 GLN cc_start: 0.8407 (tt0) cc_final: 0.8028 (tm-30) REVERT: D 687 MET cc_start: 0.7204 (tpp) cc_final: 0.6854 (mmp) REVERT: D 892 ILE cc_start: 0.8552 (tp) cc_final: 0.8200 (pt) REVERT: D 1017 MET cc_start: 0.6794 (mtt) cc_final: 0.6299 (mtt) REVERT: D 1142 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8132 (tp30) outliers start: 86 outliers final: 67 residues processed: 454 average time/residue: 0.1883 time to fit residues: 144.1612 Evaluate side-chains 468 residues out of total 3436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 387 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1012 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1002 MET Chi-restraints excluded: chain C residue 1012 TYR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1185 ILE Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1185 ILE Chi-restraints excluded: chain D residue 1227 VAL 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: 1.9990 chunk 28 optimal weight: 5.9990 chunk 320 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 453 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 151 HIS C 203 GLN C 586 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1155 HIS D 132 HIS ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1155 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105422 restraints weight = 46310.139| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.63 r_work: 0.3110 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (23 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32968 Z= 0.175 Angle : 0.572 11.450 44584 Z= 0.282 Chirality : 0.039 0.190 4980 Planarity : 0.004 0.043 5516 Dihedral : 7.921 60.167 4525 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 2.56 % Allowed : 14.53 % Favored : 82.91 % 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: 0.96 (0.14), residues: 3824 helix: 1.89 (0.11), residues: 2432 sheet: -1.49 (0.30), residues: 264 loop : -1.66 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.037 0.001 TYR D 380 PHE 0.031 0.001 PHE A1047 TRP 0.015 0.001 TRP D 763 HIS 0.018 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32968) covalent geometry : angle 0.57214 / 0.28 (44584) hydrogen bonds : bond 0.04723 / 3.22 ( 1787) hydrogen bonds : angle 3.65820 / 2.57 ( 5274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6965.75 seconds wall clock time: 120 minutes 34.00 seconds (7234.00 seconds total)