Starting phenix.real_space_refine on Mon Sep 14 15:14:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.cif" model { file = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jqo_9876/09_2026/6jqo_9876.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 156 5.16 5 C 19620 2.51 5 N 5508 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31254 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'COO': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.16, per 1000 atoms: 0.23 Number of scatterers: 31254 At special positions: 0 Unit cell: (183.04, 179.92, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 36 15.00 O 5934 8.00 N 5508 7.00 C 19620 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 53 sheets defined 38.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.689A pdb=" N ARG A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.759A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.618A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.705A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.749A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.277A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.853A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.528A pdb=" N GLY A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.842A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.888A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.605A pdb=" N GLN A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.677A pdb=" N GLU A 387 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.655A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 502 through 511 removed outlier: 4.037A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.718A pdb=" N LYS A 529 " --> pdb=" O PRO A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.544A pdb=" N GLU A 533 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 534 " --> pdb=" O PHE A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 530 through 534' Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.940A pdb=" N ILE A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.803A pdb=" N LEU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.751A pdb=" N ALA B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.548A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.582A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 93 through 118 removed outlier: 3.967A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.736A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.540A pdb=" N GLN B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.881A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.390A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.534A pdb=" N VAL B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.606A pdb=" N GLN B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.640A pdb=" N GLU B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.866A pdb=" N GLN B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.584A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 4.016A pdb=" N LYS B 458 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 459' Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.512A pdb=" N GLY B 479 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 502 through 511 removed outlier: 4.102A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 529 removed outlier: 3.541A pdb=" N LYS B 529 " --> pdb=" O PRO B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.685A pdb=" N LEU B 534 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.967A pdb=" N ILE B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.536A pdb=" N VAL B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 removed outlier: 4.033A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.654A pdb=" N LEU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.581A pdb=" N TYR C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 117 removed outlier: 4.005A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.805A pdb=" N LEU C 165 " --> pdb=" O CYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 186 through 199 removed outlier: 4.282A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.841A pdb=" N LEU C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.657A pdb=" N ALA C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 318 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 354 removed outlier: 3.516A pdb=" N GLN C 347 " --> pdb=" O ARG C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.671A pdb=" N GLU C 387 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 433 through 443 removed outlier: 3.757A pdb=" N GLN C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.526A pdb=" N GLY C 479 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.130A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.651A pdb=" N LYS C 529 " --> pdb=" O PRO C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.755A pdb=" N ILE C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.546A pdb=" N ALA C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 569 through 574' Processing helix chain 'C' and resid 583 through 596 removed outlier: 3.534A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.688A pdb=" N ALA D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.545A pdb=" N LEU D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.905A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 92 through 118 removed outlier: 3.795A pdb=" N VAL D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 removed outlier: 3.784A pdb=" N LEU D 165 " --> pdb=" O CYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 removed outlier: 3.675A pdb=" N THR D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.457A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.758A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.448A pdb=" N ALA D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.670A pdb=" N VAL D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.582A pdb=" N GLN D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.650A pdb=" N GLU D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.666A pdb=" N CYS D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.630A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 459 removed outlier: 3.924A pdb=" N LYS D 458 " --> pdb=" O GLU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.547A pdb=" N GLY D 479 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 492 Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.174A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 529 removed outlier: 3.752A pdb=" N LYS D 529 " --> pdb=" O PRO D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 534 removed outlier: 3.664A pdb=" N LEU D 534 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 removed outlier: 3.841A pdb=" N ILE D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.520A pdb=" N VAL D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 594 " --> pdb=" O ALA D 590 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 596 " --> pdb=" O ALA D 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 57 removed outlier: 3.691A pdb=" N ALA E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.608A pdb=" N LEU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 removed outlier: 3.512A pdb=" N TYR E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 117 removed outlier: 3.645A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 removed outlier: 3.897A pdb=" N LEU E 165 " --> pdb=" O CYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 175 Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.236A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 192 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.558A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 307 through 320 removed outlier: 3.621A pdb=" N ALA E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 355 removed outlier: 3.580A pdb=" N GLN E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.663A pdb=" N GLU E 387 " --> pdb=" O GLN E 384 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 411 through 418 removed outlier: 3.663A pdb=" N CYS E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.713A pdb=" N ALA E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 3.927A pdb=" N LYS E 458 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 459 " --> pdb=" O SER E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 455 through 459' Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.686A pdb=" N GLY E 479 " --> pdb=" O GLY E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 492 Processing helix chain 'E' and resid 502 through 511 removed outlier: 3.937A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 529 removed outlier: 3.789A pdb=" N LYS E 529 " --> pdb=" O PRO E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 534 removed outlier: 3.566A pdb=" N GLU E 533 " --> pdb=" O TYR E 530 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 534 " --> pdb=" O PHE E 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 530 through 534' Processing helix chain 'E' and resid 548 through 560 removed outlier: 3.933A pdb=" N ILE E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 571 through 575 removed outlier: 3.600A pdb=" N SER E 575 " --> pdb=" O ALA E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.598A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.740A pdb=" N ALA F 44 " --> pdb=" O ASP F 40 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 57 Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.518A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 removed outlier: 3.589A pdb=" N ALA F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 92 through 118 removed outlier: 3.897A pdb=" N VAL F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 114 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 175 removed outlier: 3.667A pdb=" N LEU F 165 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 187 through 199 removed outlier: 3.595A pdb=" N GLN F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 241 removed outlier: 3.765A pdb=" N MET F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.365A pdb=" N ALA F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 278 " --> pdb=" O PRO F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 Processing helix chain 'F' and resid 307 through 320 removed outlier: 3.784A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 removed outlier: 3.741A pdb=" N GLN F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.543A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 459 removed outlier: 3.926A pdb=" N LYS F 458 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 459 " --> pdb=" O SER F 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 455 through 459' Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 489 through 492 Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.010A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 529 removed outlier: 3.749A pdb=" N LYS F 529 " --> pdb=" O PRO F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 534 removed outlier: 3.695A pdb=" N LEU F 534 " --> pdb=" O PHE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 560 removed outlier: 4.079A pdb=" N ILE F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.531A pdb=" N ALA F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 593 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 594 " --> pdb=" O ALA F 590 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.573A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 125 removed outlier: 6.662A pdb=" N GLY B 425 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 452 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 427 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 426 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 265 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 299 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET B 404 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE B 301 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 406 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 303 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.530A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 152 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.606A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 299 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N MET A 404 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 301 " --> pdb=" O MET A 404 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 406 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 303 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 265 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 426 " --> pdb=" O CYS A 262 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.606A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 299 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N MET A 404 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 301 " --> pdb=" O MET A 404 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 406 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 303 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 265 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 426 " --> pdb=" O CYS A 262 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 473 removed outlier: 5.095A pdb=" N LEU A 470 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY A 485 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.893A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.617A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 671 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 608 through 609 removed outlier: 3.538A pdb=" N LEU A 609 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB5, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.682A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.848A pdb=" N ALA B 178 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 469 through 473 removed outlier: 5.243A pdb=" N LEU B 470 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 485 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 539 through 541 removed outlier: 3.960A pdb=" N ASP B 622 " --> pdb=" O MET B 547 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 539 through 541 removed outlier: 6.589A pdb=" N GLU B 650 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AC2, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.560A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AC4, first strand: chain 'C' and resid 124 through 125 removed outlier: 6.699A pdb=" N GLY D 425 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU D 452 " --> pdb=" O GLY D 425 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 427 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 426 " --> pdb=" O CYS D 262 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D 265 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG D 299 " --> pdb=" O THR D 402 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET D 404 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE D 301 " --> pdb=" O MET D 404 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA D 406 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 303 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 378 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 403 " --> pdb=" O THR D 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.479A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 378 through 379 removed outlier: 6.662A pdb=" N THR C 378 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU C 403 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 299 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET C 404 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 404 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C 406 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 303 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 265 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 426 " --> pdb=" O CYS C 262 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 378 through 379 removed outlier: 6.662A pdb=" N THR C 378 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU C 403 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG C 299 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET C 404 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 404 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C 406 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 303 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 265 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 426 " --> pdb=" O CYS C 262 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 472 through 473 Processing sheet with id=AC9, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.704A pdb=" N ASP C 622 " --> pdb=" O MET C 547 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 539 through 541 removed outlier: 6.638A pdb=" N GLU C 650 " --> pdb=" O LYS C 631 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C 605 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 673 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 603 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AD3, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.557A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 605 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR D 607 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 664 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 655 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.557A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 605 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR D 607 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 664 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 655 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 622 " --> pdb=" O MET D 547 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AD6, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.655A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.774A pdb=" N ALA D 178 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 152 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 469 through 473 removed outlier: 5.275A pdb=" N LEU D 470 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 485 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AE1, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.595A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AE3, first strand: chain 'E' and resid 124 through 125 removed outlier: 6.625A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU F 452 " --> pdb=" O GLY F 425 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU F 427 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 426 " --> pdb=" O CYS F 262 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 265 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG F 299 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET F 404 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE F 301 " --> pdb=" O MET F 404 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA F 406 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 303 " --> pdb=" O ALA F 406 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AE5, first strand: chain 'E' and resid 378 through 379 removed outlier: 6.687A pdb=" N THR E 378 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU E 403 " --> pdb=" O THR E 378 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG E 299 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET E 404 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE E 301 " --> pdb=" O MET E 404 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 406 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 303 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 300 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 426 " --> pdb=" O CYS E 262 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 378 through 379 removed outlier: 6.687A pdb=" N THR E 378 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU E 403 " --> pdb=" O THR E 378 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG E 299 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET E 404 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE E 301 " --> pdb=" O MET E 404 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 406 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 303 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 300 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 426 " --> pdb=" O CYS E 262 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AE8, first strand: chain 'E' and resid 539 through 541 removed outlier: 3.780A pdb=" N ASP E 622 " --> pdb=" O MET E 547 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 539 through 541 removed outlier: 6.575A pdb=" N GLU E 650 " --> pdb=" O LYS E 631 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AF2, first strand: chain 'E' and resid 612 through 613 Processing sheet with id=AF3, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AF4, first strand: chain 'F' and resid 20 through 23 removed outlier: 6.497A pdb=" N ARG F 20 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU F 33 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 22 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.335A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 469 through 473 removed outlier: 5.169A pdb=" N LEU F 470 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY F 485 " --> pdb=" O LEU F 470 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 539 through 541 removed outlier: 3.766A pdb=" N ASP F 622 " --> pdb=" O MET F 547 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 539 through 541 removed outlier: 6.580A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU F 671 " --> pdb=" O ILE F 604 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3036 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: 8.33 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9169 1.33 - 1.45: 4703 1.45 - 1.57: 17724 1.57 - 1.69: 66 1.69 - 1.81: 246 Bond restraints: 31908 Sorted by residual: bond pdb=" O2B NAP D 801 " pdb=" P2B NAP D 801 " ideal model delta sigma weight residual 1.736 1.606 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" O2B NAP B 801 " pdb=" P2B NAP B 801 " ideal model delta sigma weight residual 1.736 1.606 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" O2B NAP A 801 " pdb=" P2B NAP A 801 " ideal model delta sigma weight residual 1.736 1.607 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" O2B NAP F 801 " pdb=" P2B NAP F 801 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" O2B NAP E 801 " pdb=" P2B NAP E 801 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 31903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 42383 2.91 - 5.82: 785 5.82 - 8.73: 180 8.73 - 11.64: 41 11.64 - 14.55: 15 Bond angle restraints: 43404 Sorted by residual: angle pdb=" O3A COO F 802 " pdb=" P1A COO F 802 " pdb=" O5X COO F 802 " ideal model delta sigma weight residual 96.99 111.54 -14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" O3A COO B 802 " pdb=" P1A COO B 802 " pdb=" O5X COO B 802 " ideal model delta sigma weight residual 96.99 110.22 -13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O3A COO D 802 " pdb=" P1A COO D 802 " pdb=" O5X COO D 802 " ideal model delta sigma weight residual 96.99 110.03 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" O3A COO E 802 " pdb=" P1A COO E 802 " pdb=" O5X COO E 802 " ideal model delta sigma weight residual 96.99 109.66 -12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O3A COO C 802 " pdb=" P1A COO C 802 " pdb=" O5X COO C 802 " ideal model delta sigma weight residual 96.99 109.52 -12.53 3.00e+00 1.11e-01 1.74e+01 ... (remaining 43399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.46: 18338 20.46 - 40.92: 721 40.92 - 61.38: 171 61.38 - 81.85: 43 81.85 - 102.31: 29 Dihedral angle restraints: 19302 sinusoidal: 7782 harmonic: 11520 Sorted by residual: dihedral pdb=" CA GLU D 521 " pdb=" C GLU D 521 " pdb=" N ASP D 522 " pdb=" CA ASP D 522 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLU B 521 " pdb=" C GLU B 521 " pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta harmonic sigma weight residual 180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 19299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3416 0.052 - 0.103: 1141 0.103 - 0.155: 316 0.155 - 0.206: 33 0.206 - 0.258: 8 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C2B NAP E 801 " pdb=" C1B NAP E 801 " pdb=" C3B NAP E 801 " pdb=" O2B NAP E 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1B NAP E 801 " pdb=" C2B NAP E 801 " pdb=" N9A NAP E 801 " pdb=" O4B NAP E 801 " both_signs ideal model delta sigma weight residual False 2.31 2.56 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1B NAP A 801 " pdb=" C2B NAP A 801 " pdb=" N9A NAP A 801 " pdb=" O4B NAP A 801 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4911 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 COO C 802 " -0.010 2.00e-02 2.50e+03 4.90e-02 3.00e+01 pdb=" C13 COO C 802 " 0.044 2.00e-02 2.50e+03 pdb=" C2 COO C 802 " 0.060 2.00e-02 2.50e+03 pdb=" N1 COO C 802 " -0.079 2.00e-02 2.50e+03 pdb=" O2 COO C 802 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 COO D 802 " -0.045 2.00e-02 2.50e+03 4.89e-02 2.99e+01 pdb=" C4 COO D 802 " 0.016 2.00e-02 2.50e+03 pdb=" C5 COO D 802 " -0.060 2.00e-02 2.50e+03 pdb=" N2 COO D 802 " 0.077 2.00e-02 2.50e+03 pdb=" O3 COO D 802 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 COO F 802 " 0.042 2.00e-02 2.50e+03 4.51e-02 2.55e+01 pdb=" C4 COO F 802 " -0.015 2.00e-02 2.50e+03 pdb=" C5 COO F 802 " 0.055 2.00e-02 2.50e+03 pdb=" N2 COO F 802 " -0.071 2.00e-02 2.50e+03 pdb=" O3 COO F 802 " -0.011 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10004 2.85 - 3.36: 25988 3.36 - 3.87: 49967 3.87 - 4.39: 57750 4.39 - 4.90: 102692 Nonbonded interactions: 246401 Sorted by model distance: nonbonded pdb=" OG1 THR E 270 " pdb=" OD1 ASP E 272 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASP A 272 " model vdw 2.346 3.040 nonbonded pdb=" OG1 THR D 426 " pdb=" ND1 HIS D 463 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR C 270 " pdb=" OD1 ASP C 272 " model vdw 2.349 3.040 nonbonded pdb=" OD2 ASP D 127 " pdb=" ND1 HIS D 142 " model vdw 2.358 3.120 ... (remaining 246396 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.680 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.007 0.130 31908 Z= 0.331 Angle : 1.060 14.548 43404 Z= 0.504 Chirality : 0.055 0.258 4914 Planarity : 0.008 0.067 5616 Dihedral : 13.329 102.307 11898 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % 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: -3.99 (0.10), residues: 4056 helix: -3.23 (0.10), residues: 1200 sheet: -1.34 (0.19), residues: 702 loop : -2.80 (0.10), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 361 TYR 0.024 0.003 TYR E 607 PHE 0.023 0.003 PHE B 563 TRP 0.051 0.004 TRP E 124 HIS 0.010 0.002 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.33 (31908) covalent geometry : angle 1.06014 / 0.50 (43404) hydrogen bonds : bond 0.16094 / 10.95 ( 1038) hydrogen bonds : angle 7.46392 / 5.23 ( 3036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 620 time to evaluate : 1.112 Fit side-chains REVERT: A 629 THR cc_start: 0.9082 (t) cc_final: 0.8849 (m) REVERT: C 116 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7541 (mtm180) REVERT: C 632 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7953 (ttt180) REVERT: D 122 THR cc_start: 0.8957 (m) cc_final: 0.8753 (p) REVERT: D 437 GLN cc_start: 0.8111 (mt0) cc_final: 0.7863 (mt0) REVERT: E 567 MET cc_start: 0.8491 (mmp) cc_final: 0.8157 (mmm) REVERT: F 20 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7515 (mtm180) REVERT: F 159 PHE cc_start: 0.9004 (m-80) cc_final: 0.8727 (m-80) REVERT: F 309 ASN cc_start: 0.7645 (m110) cc_final: 0.7355 (m-40) outliers start: 4 outliers final: 1 residues processed: 624 average time/residue: 0.2626 time to fit residues: 240.1954 Evaluate side-chains 304 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 HIS A 347 GLN A 414 GLN A 500 GLN A 525 HIS B 158 ASN B 347 GLN B 433 GLN B 463 HIS B 500 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 158 ASN C 433 GLN C 500 GLN C 525 HIS D 433 GLN D 450 GLN D 500 GLN D 554 ASN E 158 ASN E 347 GLN E 500 GLN ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 HIS F 433 GLN F 500 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.087540 restraints weight = 41114.503| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.72 r_work: 0.2693 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31908 Z= 0.137 Angle : 0.593 11.105 43404 Z= 0.303 Chirality : 0.044 0.158 4914 Planarity : 0.006 0.048 5616 Dihedral : 12.831 98.865 4849 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.17 % Allowed : 6.81 % Favored : 92.03 % 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: -2.84 (0.11), residues: 4056 helix: -1.70 (0.13), residues: 1260 sheet: -0.84 (0.19), residues: 708 loop : -2.41 (0.11), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 477 TYR 0.021 0.002 TYR D 607 PHE 0.029 0.002 PHE E 595 TRP 0.032 0.002 TRP C 124 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (31908) covalent geometry : angle 0.59328 / 0.30 (43404) hydrogen bonds : bond 0.03930 / 2.61 ( 1038) hydrogen bonds : angle 5.19607 / 3.63 ( 3036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 1.092 Fit side-chains REVERT: A 281 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7836 (ttp-170) REVERT: A 330 GLU cc_start: 0.7157 (tp30) cc_final: 0.6577 (tt0) REVERT: A 505 MET cc_start: 0.9243 (tpp) cc_final: 0.8778 (mmt) REVERT: A 629 THR cc_start: 0.9249 (t) cc_final: 0.8930 (m) REVERT: B 281 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7814 (ttt-90) REVERT: B 467 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 122 THR cc_start: 0.9069 (m) cc_final: 0.8714 (p) REVERT: D 281 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7759 (ttt-90) REVERT: E 33 GLU cc_start: 0.8182 (pp20) cc_final: 0.7921 (pp20) REVERT: E 330 GLU cc_start: 0.6990 (tp30) cc_final: 0.6748 (tt0) REVERT: E 441 ASP cc_start: 0.8495 (m-30) cc_final: 0.8154 (m-30) REVERT: E 622 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: F 20 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7448 (mtm180) REVERT: F 159 PHE cc_start: 0.9070 (m-80) cc_final: 0.8793 (m-80) REVERT: F 281 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7825 (ttt-90) outliers start: 37 outliers final: 18 residues processed: 339 average time/residue: 0.2497 time to fit residues: 127.8153 Evaluate side-chains 281 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 175 optimal weight: 3.9990 chunk 264 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 HIS B 339 ASN C 347 GLN D 24 HIS D 329 GLN D 566 HIS E 525 HIS F 24 HIS ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.083925 restraints weight = 41243.048| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.64 r_work: 0.2724 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31908 Z= 0.179 Angle : 0.612 9.313 43404 Z= 0.311 Chirality : 0.045 0.158 4914 Planarity : 0.005 0.045 5616 Dihedral : 11.930 105.791 4849 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.35 % Allowed : 8.19 % Favored : 90.45 % 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: -2.17 (0.12), residues: 4056 helix: -0.84 (0.14), residues: 1248 sheet: -0.55 (0.19), residues: 726 loop : -2.19 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 141 TYR 0.022 0.002 TYR C 607 PHE 0.025 0.002 PHE E 595 TRP 0.021 0.002 TRP A 124 HIS 0.005 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (31908) covalent geometry : angle 0.61194 / 0.31 (43404) hydrogen bonds : bond 0.04122 / 2.74 ( 1038) hydrogen bonds : angle 5.00611 / 3.48 ( 3036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8769 (t0) cc_final: 0.8346 (t0) REVERT: A 281 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7982 (ttp-170) REVERT: B 281 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7987 (ttt-90) REVERT: D 122 THR cc_start: 0.9160 (m) cc_final: 0.8842 (p) REVERT: D 281 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8010 (ttt-90) REVERT: E 441 ASP cc_start: 0.8615 (m-30) cc_final: 0.8270 (m-30) REVERT: F 20 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7717 (mtm180) REVERT: F 33 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8038 (pp20) REVERT: F 159 PHE cc_start: 0.9116 (m-80) cc_final: 0.8823 (m-80) REVERT: F 281 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8008 (ttt-90) outliers start: 43 outliers final: 29 residues processed: 297 average time/residue: 0.2383 time to fit residues: 106.0374 Evaluate side-chains 282 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 341 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 334 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS B 339 ASN ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.079769 restraints weight = 41668.925| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.81 r_work: 0.2624 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 31908 Z= 0.157 Angle : 0.573 9.377 43404 Z= 0.291 Chirality : 0.044 0.155 4914 Planarity : 0.005 0.043 5616 Dihedral : 11.319 107.496 4849 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.70 % Allowed : 9.14 % Favored : 89.16 % 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: -1.75 (0.12), residues: 4056 helix: -0.32 (0.15), residues: 1248 sheet: -0.36 (0.19), residues: 714 loop : -2.02 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 410 TYR 0.020 0.002 TYR D 607 PHE 0.023 0.002 PHE E 595 TRP 0.013 0.001 TRP B 124 HIS 0.004 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (31908) covalent geometry : angle 0.57264 / 0.29 (43404) hydrogen bonds : bond 0.03732 / 2.46 ( 1038) hydrogen bonds : angle 4.80886 / 3.34 ( 3036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 1.302 Fit side-chains REVERT: A 120 ASP cc_start: 0.8918 (t0) cc_final: 0.8522 (t0) REVERT: A 281 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7877 (ttp-170) REVERT: A 522 ASP cc_start: 0.7857 (t0) cc_final: 0.7357 (t0) REVERT: B 29 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: B 648 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8784 (p) REVERT: C 122 THR cc_start: 0.9192 (m) cc_final: 0.8721 (p) REVERT: C 313 ASP cc_start: 0.7883 (m-30) cc_final: 0.7682 (m-30) REVERT: D 29 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: D 122 THR cc_start: 0.9100 (m) cc_final: 0.8788 (p) REVERT: E 287 MET cc_start: 0.8639 (ttp) cc_final: 0.8411 (ttm) REVERT: E 330 GLU cc_start: 0.7081 (tp30) cc_final: 0.6697 (tt0) REVERT: E 441 ASP cc_start: 0.8502 (m-30) cc_final: 0.8150 (m-30) REVERT: F 20 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7679 (mtm180) REVERT: F 33 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: F 159 PHE cc_start: 0.9074 (m-80) cc_final: 0.8774 (m-80) REVERT: F 281 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7833 (ttt-90) outliers start: 54 outliers final: 30 residues processed: 311 average time/residue: 0.2596 time to fit residues: 122.0244 Evaluate side-chains 288 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 218 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 365 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.082557 restraints weight = 41200.248| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.63 r_work: 0.2674 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 31908 Z= 0.196 Angle : 0.607 9.461 43404 Z= 0.308 Chirality : 0.045 0.159 4914 Planarity : 0.005 0.044 5616 Dihedral : 11.069 108.832 4849 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.95 % Allowed : 9.83 % Favored : 88.22 % 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: -1.57 (0.12), residues: 4056 helix: -0.08 (0.15), residues: 1248 sheet: -0.33 (0.19), residues: 714 loop : -1.94 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 141 TYR 0.021 0.002 TYR C 607 PHE 0.022 0.002 PHE E 595 TRP 0.012 0.002 TRP E 32 HIS 0.006 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (31908) covalent geometry : angle 0.60662 / 0.31 (43404) hydrogen bonds : bond 0.04092 / 2.71 ( 1038) hydrogen bonds : angle 4.87028 / 3.39 ( 3036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 1.208 Fit side-chains REVERT: A 281 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8042 (ttp-170) REVERT: A 522 ASP cc_start: 0.7944 (t0) cc_final: 0.7554 (t0) REVERT: B 522 ASP cc_start: 0.8068 (t70) cc_final: 0.7714 (t0) REVERT: B 622 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8253 (t0) REVERT: B 648 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8837 (p) REVERT: C 122 THR cc_start: 0.9292 (m) cc_final: 0.8850 (p) REVERT: D 29 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: D 122 THR cc_start: 0.9163 (m) cc_final: 0.8881 (p) REVERT: D 243 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: D 281 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8029 (ttt-90) REVERT: E 395 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: E 441 ASP cc_start: 0.8653 (m-30) cc_final: 0.8341 (m-30) REVERT: F 20 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7889 (mtm180) REVERT: F 33 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8138 (pp20) REVERT: F 134 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8542 (mmtm) REVERT: F 159 PHE cc_start: 0.9152 (m-80) cc_final: 0.8882 (m-80) outliers start: 62 outliers final: 35 residues processed: 312 average time/residue: 0.2509 time to fit residues: 118.4382 Evaluate side-chains 294 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 135 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 393 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 398 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS C 659 HIS F 158 ASN F 566 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.085169 restraints weight = 41012.270| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.56 r_work: 0.2701 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31908 Z= 0.142 Angle : 0.550 9.327 43404 Z= 0.281 Chirality : 0.043 0.152 4914 Planarity : 0.004 0.044 5616 Dihedral : 10.549 108.770 4849 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.83 % Allowed : 10.65 % Favored : 87.52 % 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: -1.35 (0.13), residues: 4056 helix: 0.14 (0.15), residues: 1260 sheet: -0.23 (0.19), residues: 714 loop : -1.83 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.020 0.002 TYR C 607 PHE 0.022 0.001 PHE E 595 TRP 0.010 0.001 TRP A 32 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (31908) covalent geometry : angle 0.54970 / 0.28 (43404) hydrogen bonds : bond 0.03529 / 2.33 ( 1038) hydrogen bonds : angle 4.68875 / 3.26 ( 3036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 1.134 Fit side-chains REVERT: A 120 ASP cc_start: 0.8791 (t0) cc_final: 0.8536 (t0) REVERT: A 281 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8042 (ttp-170) REVERT: A 522 ASP cc_start: 0.7949 (t0) cc_final: 0.7494 (t0) REVERT: B 622 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8179 (t0) REVERT: B 648 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 122 THR cc_start: 0.9274 (m) cc_final: 0.8831 (p) REVERT: D 29 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: D 122 THR cc_start: 0.9152 (m) cc_final: 0.8862 (p) REVERT: D 281 ARG cc_start: 0.8262 (ttp80) cc_final: 0.8031 (ttt-90) REVERT: E 330 GLU cc_start: 0.7150 (tp30) cc_final: 0.6800 (tt0) REVERT: E 395 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: E 441 ASP cc_start: 0.8594 (m-30) cc_final: 0.8275 (m-30) REVERT: F 20 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7860 (mtm180) REVERT: F 33 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (pp20) REVERT: F 159 PHE cc_start: 0.9152 (m-80) cc_final: 0.8902 (m-80) REVERT: F 243 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: F 281 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8144 (ttt-90) outliers start: 58 outliers final: 40 residues processed: 305 average time/residue: 0.2549 time to fit residues: 117.4544 Evaluate side-chains 296 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 518 LYS Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 0.0970 chunk 262 optimal weight: 2.9990 chunk 113 optimal weight: 0.0020 chunk 350 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 346 optimal weight: 0.4980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS B 659 HIS C 472 HIS E 3 GLN E 472 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.088942 restraints weight = 40928.900| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.60 r_work: 0.2793 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31908 Z= 0.085 Angle : 0.483 9.758 43404 Z= 0.246 Chirality : 0.041 0.141 4914 Planarity : 0.004 0.047 5616 Dihedral : 9.711 104.077 4849 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 11.50 % Favored : 87.30 % 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: -0.99 (0.13), residues: 4056 helix: 0.54 (0.15), residues: 1260 sheet: 0.04 (0.20), residues: 702 loop : -1.71 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 410 TYR 0.020 0.001 TYR E 607 PHE 0.024 0.001 PHE E 595 TRP 0.006 0.001 TRP A 32 HIS 0.004 0.000 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (31908) covalent geometry : angle 0.48305 / 0.25 (43404) hydrogen bonds : bond 0.02646 / 1.73 ( 1038) hydrogen bonds : angle 4.34723 / 3.03 ( 3036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 1.224 Fit side-chains REVERT: A 281 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8039 (ttp-170) REVERT: A 410 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8051 (mmm-85) REVERT: A 522 ASP cc_start: 0.7659 (t0) cc_final: 0.7450 (t0) REVERT: A 629 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8906 (m) REVERT: C 122 THR cc_start: 0.9193 (m) cc_final: 0.8660 (p) REVERT: C 239 MET cc_start: 0.8913 (tmm) cc_final: 0.8666 (ppp) REVERT: C 278 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7300 (pp) REVERT: D 29 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: D 243 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: D 281 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7885 (ttt-90) REVERT: E 330 GLU cc_start: 0.7353 (tp30) cc_final: 0.6879 (tt0) REVERT: E 410 ARG cc_start: 0.7994 (tpm170) cc_final: 0.7719 (mmm-85) REVERT: E 441 ASP cc_start: 0.8553 (m-30) cc_final: 0.8219 (m-30) REVERT: F 20 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7826 (mtm180) REVERT: F 33 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: F 101 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7949 (mm-30) REVERT: F 159 PHE cc_start: 0.9134 (m-80) cc_final: 0.8863 (m-80) REVERT: F 281 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8071 (ttt-90) outliers start: 38 outliers final: 16 residues processed: 332 average time/residue: 0.2411 time to fit residues: 123.1066 Evaluate side-chains 281 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 518 LYS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 169 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.103579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.078724 restraints weight = 42261.215| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.73 r_work: 0.2586 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31908 Z= 0.203 Angle : 0.609 9.992 43404 Z= 0.308 Chirality : 0.046 0.186 4914 Planarity : 0.005 0.043 5616 Dihedral : 10.128 98.497 4849 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.51 % Allowed : 11.44 % Favored : 87.05 % 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: -1.07 (0.13), residues: 4056 helix: 0.52 (0.15), residues: 1248 sheet: -0.19 (0.19), residues: 732 loop : -1.72 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 410 TYR 0.024 0.002 TYR C 607 PHE 0.022 0.002 PHE E 595 TRP 0.015 0.002 TRP B 32 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.20 (31908) covalent geometry : angle 0.60891 / 0.31 (43404) hydrogen bonds : bond 0.04041 / 2.68 ( 1038) hydrogen bonds : angle 4.75132 / 3.30 ( 3036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.210 Fit side-chains REVERT: A 281 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7904 (ttp-170) REVERT: A 522 ASP cc_start: 0.7784 (t0) cc_final: 0.7156 (t0) REVERT: B 522 ASP cc_start: 0.7916 (t70) cc_final: 0.7506 (t0) REVERT: B 648 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8757 (p) REVERT: C 122 THR cc_start: 0.9222 (m) cc_final: 0.8830 (p) REVERT: D 29 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: D 243 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: D 281 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7744 (ttt-90) REVERT: E 410 ARG cc_start: 0.8146 (tpm170) cc_final: 0.7636 (mmm-85) REVERT: E 441 ASP cc_start: 0.8462 (m-30) cc_final: 0.8138 (m-30) REVERT: F 20 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7652 (mtm180) REVERT: F 33 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: F 159 PHE cc_start: 0.9052 (m-80) cc_final: 0.8753 (m-80) REVERT: F 243 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: F 281 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7878 (ttt-90) outliers start: 48 outliers final: 31 residues processed: 295 average time/residue: 0.2563 time to fit residues: 114.1671 Evaluate side-chains 282 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 231 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 378 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 392 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.086183 restraints weight = 41037.550| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.56 r_work: 0.2742 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31908 Z= 0.119 Angle : 0.537 10.287 43404 Z= 0.272 Chirality : 0.043 0.149 4914 Planarity : 0.004 0.044 5616 Dihedral : 9.729 98.018 4849 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.32 % Allowed : 11.59 % Favored : 87.08 % 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: -0.90 (0.13), residues: 4056 helix: 0.66 (0.15), residues: 1260 sheet: -0.06 (0.19), residues: 714 loop : -1.64 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 410 TYR 0.020 0.002 TYR C 607 PHE 0.023 0.001 PHE E 595 TRP 0.010 0.001 TRP A 32 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (31908) covalent geometry : angle 0.53737 / 0.27 (43404) hydrogen bonds : bond 0.03167 / 2.08 ( 1038) hydrogen bonds : angle 4.50340 / 3.13 ( 3036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 1.188 Fit side-chains REVERT: A 281 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8040 (ttp-170) REVERT: B 334 MET cc_start: 0.8764 (ttm) cc_final: 0.8552 (ttp) REVERT: B 648 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (p) REVERT: C 122 THR cc_start: 0.9284 (m) cc_final: 0.8867 (p) REVERT: C 239 MET cc_start: 0.8894 (tmm) cc_final: 0.8680 (ppp) REVERT: D 29 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: D 193 MET cc_start: 0.8861 (mtt) cc_final: 0.8637 (mtt) REVERT: D 243 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: D 281 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8009 (ttt-90) REVERT: E 345 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: E 410 ARG cc_start: 0.8095 (tpm170) cc_final: 0.7745 (mmm-85) REVERT: E 441 ASP cc_start: 0.8528 (m-30) cc_final: 0.8227 (m-30) REVERT: F 20 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7866 (mtm180) REVERT: F 33 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: F 159 PHE cc_start: 0.9144 (m-80) cc_final: 0.8891 (m-80) REVERT: F 243 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: F 281 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8082 (ttt-90) outliers start: 42 outliers final: 26 residues processed: 292 average time/residue: 0.2502 time to fit residues: 111.1419 Evaluate side-chains 281 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 644 LYS Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 518 LYS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 293 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 337 optimal weight: 8.9990 chunk 342 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.085410 restraints weight = 40942.433| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.56 r_work: 0.2731 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31908 Z= 0.138 Angle : 0.554 10.220 43404 Z= 0.280 Chirality : 0.043 0.149 4914 Planarity : 0.004 0.042 5616 Dihedral : 9.623 94.541 4849 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 11.81 % Favored : 86.99 % 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 (0.13), residues: 4056 helix: 0.73 (0.15), residues: 1260 sheet: -0.06 (0.19), residues: 714 loop : -1.61 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 410 TYR 0.021 0.002 TYR C 607 PHE 0.022 0.001 PHE E 595 TRP 0.011 0.001 TRP B 32 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (31908) covalent geometry : angle 0.55366 / 0.28 (43404) hydrogen bonds : bond 0.03392 / 2.24 ( 1038) hydrogen bonds : angle 4.55250 / 3.17 ( 3036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.236 Fit side-chains REVERT: A 281 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8105 (ttp-170) REVERT: A 410 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: B 334 MET cc_start: 0.8786 (ttm) cc_final: 0.8585 (ttp) REVERT: B 648 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 122 THR cc_start: 0.9265 (m) cc_final: 0.8854 (p) REVERT: C 239 MET cc_start: 0.8904 (tmm) cc_final: 0.8668 (ppp) REVERT: D 29 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: D 243 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: D 281 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8024 (ttt-90) REVERT: E 33 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7713 (pp20) REVERT: E 345 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: E 410 ARG cc_start: 0.8107 (tpm170) cc_final: 0.7744 (mmm-85) REVERT: E 441 ASP cc_start: 0.8535 (m-30) cc_final: 0.8233 (m-30) REVERT: F 20 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7899 (mtm180) REVERT: F 33 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: F 101 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8133 (mm-30) REVERT: F 159 PHE cc_start: 0.9114 (m-80) cc_final: 0.8836 (m-80) REVERT: F 243 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: F 281 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8092 (ttt-90) outliers start: 38 outliers final: 26 residues processed: 283 average time/residue: 0.2598 time to fit residues: 111.0428 Evaluate side-chains 282 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 0.0670 chunk 303 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 281 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.086965 restraints weight = 40989.171| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.56 r_work: 0.2757 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31908 Z= 0.109 Angle : 0.522 10.287 43404 Z= 0.264 Chirality : 0.042 0.145 4914 Planarity : 0.004 0.043 5616 Dihedral : 9.207 91.674 4849 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 11.88 % Favored : 86.93 % 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: -0.73 (0.13), residues: 4056 helix: 0.88 (0.15), residues: 1260 sheet: 0.01 (0.19), residues: 714 loop : -1.58 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 410 TYR 0.020 0.002 TYR C 607 PHE 0.023 0.001 PHE E 595 TRP 0.008 0.001 TRP B 32 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (31908) covalent geometry : angle 0.52197 / 0.26 (43404) hydrogen bonds : bond 0.03003 / 1.97 ( 1038) hydrogen bonds : angle 4.41393 / 3.08 ( 3036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7868.54 seconds wall clock time: 135 minutes 38.64 seconds (8138.64 seconds total)