Starting phenix.real_space_refine on Fri Sep 19 09:15:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsl_61776/09_2025/9jsl_61776.map" } resolution = 3.59 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= 0.012 sd= 0.084 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 Ca 21 9.91 5 S 39 5.16 5 C 16181 2.51 5 N 4063 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25496 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3488 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3481 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3830 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3836 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3852 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.87, per 1000 atoms: 0.27 Number of scatterers: 25496 At special positions: 0 Unit cell: (176.88, 176, 96.8, 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) Ca 21 19.99 S 39 16.00 O 5192 8.00 N 4063 7.00 C 16181 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: 2.01 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 66 sheets defined 17.5% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.641A pdb=" N ASN A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.150A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.579A pdb=" N SER A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 504 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.663A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.744A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 658 through 662 removed outlier: 4.129A pdb=" N LYS A 661 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.635A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.825A pdb=" N ASN B 504 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.705A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.831A pdb=" N LYS B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'B' and resid 658 through 662 removed outlier: 3.933A pdb=" N LYS B 661 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.824A pdb=" N ASN C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.618A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 removed outlier: 3.983A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.806A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.614A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 removed outlier: 3.629A pdb=" N LYS D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 504 Processing helix chain 'D' and resid 505 through 511 removed outlier: 3.553A pdb=" N ILE D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.986A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 658 through 662 removed outlier: 4.113A pdb=" N LYS D 661 " --> pdb=" O PRO D 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 245 through 249 removed outlier: 3.792A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 463 through 472 removed outlier: 4.059A pdb=" N LYS E 467 " --> pdb=" O TYR E 463 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 511 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 580 through 592 removed outlier: 3.753A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'E' and resid 658 through 662 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 252 removed outlier: 4.035A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 331 through 337 removed outlier: 3.685A pdb=" N THR F 335 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 416 removed outlier: 3.870A pdb=" N GLU F 416 " --> pdb=" O LEU F 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 413 through 416' Processing helix chain 'F' and resid 462 through 471 removed outlier: 3.715A pdb=" N SER F 471 " --> pdb=" O LYS F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 505 removed outlier: 3.806A pdb=" N ASN F 504 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 4.220A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 658 through 662 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.766A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 379 removed outlier: 4.089A pdb=" N LEU G 378 " --> pdb=" O TRP G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.662A pdb=" N GLY G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 504 removed outlier: 3.828A pdb=" N ASN G 504 " --> pdb=" O SER G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 501 through 504' Processing helix chain 'G' and resid 505 through 510 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 3.649A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 removed outlier: 3.505A pdb=" N VAL G 602 " --> pdb=" O ILE G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 658 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 309 removed outlier: 4.973A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 422 removed outlier: 7.048A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 408 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.324A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 657 removed outlier: 5.852A pdb=" N ASN A 647 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 730 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 649 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 728 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 651 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 722 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 657 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 720 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.600A pdb=" N ILE B 240 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.179A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 438 " --> pdb=" O TYR B 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.179A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 390 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 422 removed outlier: 6.950A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 417 through 422 removed outlier: 6.950A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 478 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 412 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 530 Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.848A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 617 through 619 removed outlier: 3.550A pdb=" N THR B 684 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 647 through 656 removed outlier: 5.861A pdb=" N ASN B 647 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE B 730 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 649 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY B 728 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 651 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 667 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 309 removed outlier: 5.558A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 309 removed outlier: 5.558A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.799A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 412 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.262A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 613 " --> pdb=" O GLU C 576 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU C 576 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.518A pdb=" N TYR C 564 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 559 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AC9, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.834A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 738 " --> pdb=" O VAL C 669 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD2, first strand: chain 'D' and resid 299 through 307 removed outlier: 6.405A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 417 through 422 removed outlier: 6.956A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 412 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU D 477 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD5, first strand: chain 'D' and resid 524 through 530 removed outlier: 3.552A pdb=" N LYS D 613 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU D 576 " --> pdb=" O LYS D 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 557 through 559 removed outlier: 3.884A pdb=" N LEU D 562 " --> pdb=" O ASN D 559 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.624A pdb=" N THR D 684 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 647 through 657 removed outlier: 5.868A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 657 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE D 720 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG D 667 " --> pdb=" O LEU D 740 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE1, first strand: chain 'E' and resid 299 through 306 removed outlier: 3.589A pdb=" N GLY E 302 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU E 304 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 299 through 306 removed outlier: 3.589A pdb=" N GLY E 302 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU E 304 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 326 through 329 removed outlier: 3.782A pdb=" N THR E 327 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER E 363 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 351 through 352 removed outlier: 6.109A pdb=" N ASN E 351 " --> pdb=" O PHE E 579 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 576 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 417 through 422 removed outlier: 7.140A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 417 through 422 removed outlier: 7.140A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS E 404 " --> pdb=" O ASN E 485 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN E 485 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN E 481 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN E 410 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR E 479 " --> pdb=" O ASN E 410 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 557 through 559 removed outlier: 3.997A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AE9, first strand: chain 'E' and resid 617 through 619 removed outlier: 5.584A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG E 667 " --> pdb=" O LEU E 740 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 652 through 657 removed outlier: 4.108A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 657 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 721 " --> pdb=" O LYS E 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN E 686 " --> pdb=" O THR E 723 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS E 693 " --> pdb=" O ILE E 687 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AF3, first strand: chain 'F' and resid 299 through 303 removed outlier: 3.733A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 299 through 303 removed outlier: 3.733A pdb=" N GLY F 302 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 326 through 329 removed outlier: 3.523A pdb=" N SER F 363 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 351 through 352 removed outlier: 6.493A pdb=" N ASN F 351 " --> pdb=" O PHE F 579 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 420 through 422 removed outlier: 4.278A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF9, first strand: chain 'F' and resid 564 through 565 Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.513A pdb=" N ASP F 695 " --> pdb=" O VAL F 685 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 693 " --> pdb=" O ILE F 687 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 647 through 657 removed outlier: 4.252A pdb=" N GLY F 651 " --> pdb=" O GLY F 728 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY F 728 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR F 653 " --> pdb=" O SER F 726 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER F 726 " --> pdb=" O THR F 653 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 655 " --> pdb=" O LEU F 724 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU F 724 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE F 657 " --> pdb=" O ILE F 722 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 722 " --> pdb=" O ILE F 657 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG F 667 " --> pdb=" O LEU F 740 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG4, first strand: chain 'G' and resid 299 through 306 removed outlier: 5.149A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 299 through 306 removed outlier: 5.149A pdb=" N VAL G 301 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR G 395 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N MET G 303 " --> pdb=" O ARG G 393 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG G 393 " --> pdb=" O MET G 303 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 326 through 329 Processing sheet with id=AG7, first strand: chain 'G' and resid 403 through 411 removed outlier: 4.286A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 524 through 530 removed outlier: 9.381A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.734A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 617 through 619 removed outlier: 3.632A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 617 through 619 removed outlier: 3.632A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.562A pdb=" N ILE G 722 " --> pdb=" O ILE G 655 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU G 721 " --> pdb=" O LYS G 688 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.77 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4588 1.28 - 1.41: 5557 1.41 - 1.55: 15661 1.55 - 1.68: 19 1.68 - 1.81: 71 Bond restraints: 25896 Sorted by residual: bond pdb=" C GLU G 548 " pdb=" O GLU G 548 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.16e-02 7.43e+03 5.50e+01 bond pdb=" C GLU G 548 " pdb=" N ALA G 549 " ideal model delta sigma weight residual 1.335 1.268 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C GLY G 547 " pdb=" N GLU G 548 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.33e-02 5.65e+03 1.31e+01 bond pdb=" CA GLU G 548 " pdb=" C GLU G 548 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.26e-02 6.30e+03 5.10e+00 bond pdb=" CD2 TRP E 374 " pdb=" CE2 TRP E 374 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.87e+00 ... (remaining 25891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 34361 1.65 - 3.31: 512 3.31 - 4.96: 63 4.96 - 6.61: 18 6.61 - 8.26: 5 Bond angle restraints: 34959 Sorted by residual: angle pdb=" N GLU G 548 " pdb=" CA GLU G 548 " pdb=" C GLU G 548 " ideal model delta sigma weight residual 111.14 103.71 7.43 1.08e+00 8.57e-01 4.73e+01 angle pdb=" C GLU G 548 " pdb=" CA GLU G 548 " pdb=" CB GLU G 548 " ideal model delta sigma weight residual 110.90 118.45 -7.55 1.58e+00 4.01e-01 2.29e+01 angle pdb=" N VAL D 512 " pdb=" CA VAL D 512 " pdb=" C VAL D 512 " ideal model delta sigma weight residual 113.20 108.87 4.33 9.60e-01 1.09e+00 2.03e+01 angle pdb=" CD2 TRP F 374 " pdb=" CE3 TRP F 374 " pdb=" CZ3 TRP F 374 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP B 631 " pdb=" CE3 TRP B 631 " pdb=" CZ3 TRP B 631 " ideal model delta sigma weight residual 118.60 123.98 -5.38 1.30e+00 5.92e-01 1.71e+01 ... (remaining 34954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14181 17.96 - 35.92: 1257 35.92 - 53.88: 213 53.88 - 71.83: 45 71.83 - 89.79: 29 Dihedral angle restraints: 15725 sinusoidal: 6252 harmonic: 9473 Sorted by residual: dihedral pdb=" CA ILE C 459 " pdb=" C ILE C 459 " pdb=" N PRO C 460 " pdb=" CA PRO C 460 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB GLU G 700 " pdb=" CG GLU G 700 " pdb=" CD GLU G 700 " pdb=" OE1 GLU G 700 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU F 691 " pdb=" CG GLU F 691 " pdb=" CD GLU F 691 " pdb=" OE1 GLU F 691 " ideal model delta sinusoidal sigma weight residual 0.00 -89.37 89.37 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2613 0.033 - 0.066: 904 0.066 - 0.099: 307 0.099 - 0.133: 209 0.133 - 0.166: 8 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CA GLU G 548 " pdb=" N GLU G 548 " pdb=" C GLU G 548 " pdb=" CB GLU G 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB ILE D 657 " pdb=" CA ILE D 657 " pdb=" CG1 ILE D 657 " pdb=" CG2 ILE D 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE A 657 " pdb=" CA ILE A 657 " pdb=" CG1 ILE A 657 " pdb=" CG2 ILE A 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 4038 not shown) Planarity restraints: 4553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 548 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLU G 548 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU G 548 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA G 549 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO D 269 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 698 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO F 699 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 699 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 699 " -0.033 5.00e-02 4.00e+02 ... (remaining 4550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3514 2.76 - 3.29: 24135 3.29 - 3.83: 39974 3.83 - 4.36: 47271 4.36 - 4.90: 84270 Nonbonded interactions: 199164 Sorted by model distance: nonbonded pdb=" O LYS G 468 " pdb=" OG SER G 471 " model vdw 2.224 3.040 nonbonded pdb=" OG SER C 259 " pdb=" OE1 GLU C 262 " model vdw 2.228 3.040 nonbonded pdb=" O ASP C 581 " pdb=" OG SER C 584 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU B 287 " pdb=" NE ARG B 527 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU E 572 " pdb=" NZ LYS E 598 " model vdw 2.255 3.120 ... (remaining 199159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 903)) selection = (chain 'B' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'C' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'D' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'E' and (resid 216 through 308 or resid 342 or resid 388 through 449 or r \ esid 460 through 614 or (resid 615 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 616 through 741 or resid 901 through 903)) selection = (chain 'F' and (resid 216 through 307 or resid 340 or resid 365 or resid 380 thr \ ough 449 or resid 460 through 614 or (resid 615 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 616 through 741 or resid 901 throug \ h 903)) selection = (chain 'G' and (resid 216 through 308 or resid 365 or resid 380 through 381 or r \ esid 390 through 449 or resid 460 through 614 or (resid 615 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 616 through 741 or resi \ d 901 through 903)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.860 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.002 0.086 25896 Z= 0.138 Angle : 0.512 8.263 34959 Z= 0.304 Chirality : 0.043 0.166 4041 Planarity : 0.004 0.060 4553 Dihedral : 14.393 89.793 9527 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.14 % Allowed : 0.48 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.36 (0.14), residues: 3251 helix: -0.83 (0.24), residues: 454 sheet: 1.42 (0.20), residues: 726 loop : -0.73 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 606 TYR 0.013 0.001 TYR D 296 PHE 0.008 0.001 PHE F 670 TRP 0.005 0.001 TRP G 631 HIS 0.001 0.000 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00250 (25896) covalent geometry : angle 0.51175 (34959) hydrogen bonds : bond 0.25355 ( 711) hydrogen bonds : angle 9.41245 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.4870 (ttt) cc_final: 0.4569 (ptt) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.1631 time to fit residues: 84.8050 Evaluate side-chains 172 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain D residue 296 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 30.0000 overall best weight: 3.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 508 GLN B 734 ASN C 638 ASN D 391 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 ASN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 523 GLN G 633 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059316 restraints weight = 96062.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.061056 restraints weight = 50912.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062164 restraints weight = 34294.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062865 restraints weight = 26800.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063289 restraints weight = 23079.294| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25896 Z= 0.142 Angle : 0.550 10.573 34959 Z= 0.309 Chirality : 0.044 0.172 4041 Planarity : 0.004 0.054 4553 Dihedral : 3.906 50.080 3281 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.65 % Allowed : 6.95 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.22 (0.14), residues: 3251 helix: -0.44 (0.25), residues: 455 sheet: 1.35 (0.19), residues: 731 loop : -0.64 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 289 TYR 0.015 0.001 TYR G 665 PHE 0.019 0.001 PHE C 670 TRP 0.007 0.001 TRP G 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00299 (25896) covalent geometry : angle 0.54967 (34959) hydrogen bonds : bond 0.03773 ( 711) hydrogen bonds : angle 6.16036 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7886 (tpt) cc_final: 0.7562 (tpt) REVERT: A 608 MET cc_start: 0.9332 (mtp) cc_final: 0.8915 (mtp) REVERT: B 268 ASP cc_start: 0.8297 (p0) cc_final: 0.8084 (p0) REVERT: C 451 MET cc_start: 0.6092 (ttt) cc_final: 0.5001 (ptt) REVERT: E 476 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7492 (mmmt) REVERT: F 303 MET cc_start: 0.8953 (ptm) cc_final: 0.8375 (ppp) REVERT: G 608 MET cc_start: 0.8991 (mtp) cc_final: 0.8462 (mtp) outliers start: 19 outliers final: 9 residues processed: 186 average time/residue: 0.1534 time to fit residues: 48.4185 Evaluate side-chains 151 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 309 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN C 609 ASN D 391 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056467 restraints weight = 97337.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058068 restraints weight = 53734.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059090 restraints weight = 37110.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059737 restraints weight = 29491.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060102 restraints weight = 25606.646| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25896 Z= 0.183 Angle : 0.549 10.760 34959 Z= 0.309 Chirality : 0.044 0.160 4041 Planarity : 0.004 0.052 4553 Dihedral : 4.078 50.302 3277 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.82 % Allowed : 9.69 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.36 (0.14), residues: 3251 helix: -0.38 (0.25), residues: 455 sheet: 1.11 (0.19), residues: 741 loop : -0.72 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.014 0.001 TYR G 665 PHE 0.010 0.001 PHE B 618 TRP 0.006 0.001 TRP C 631 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00393 (25896) covalent geometry : angle 0.54883 (34959) hydrogen bonds : bond 0.03356 ( 711) hydrogen bonds : angle 5.60831 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7795 (tpt) cc_final: 0.7438 (tpt) REVERT: A 608 MET cc_start: 0.9301 (mtp) cc_final: 0.8847 (mtp) REVERT: B 586 ILE cc_start: 0.9185 (mt) cc_final: 0.8929 (mm) REVERT: C 451 MET cc_start: 0.6423 (ttt) cc_final: 0.5332 (ptt) REVERT: C 608 MET cc_start: 0.8362 (mtm) cc_final: 0.7947 (mtm) REVERT: C 720 ILE cc_start: 0.7543 (mm) cc_final: 0.7157 (tt) REVERT: C 730 ILE cc_start: 0.7640 (pt) cc_final: 0.7306 (tp) REVERT: E 476 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7657 (mmmt) REVERT: E 519 ASP cc_start: 0.8744 (t0) cc_final: 0.8510 (m-30) REVERT: E 659 MET cc_start: 0.7750 (tmm) cc_final: 0.7336 (tmm) REVERT: E 716 ASP cc_start: 0.8271 (m-30) cc_final: 0.7957 (m-30) REVERT: F 303 MET cc_start: 0.8860 (ptm) cc_final: 0.8467 (ppp) REVERT: G 543 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7388 (mp0) outliers start: 24 outliers final: 18 residues processed: 171 average time/residue: 0.1465 time to fit residues: 42.6674 Evaluate side-chains 159 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 189 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN C 431 ASN D 431 ASN D 494 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 686 ASN E 734 ASN F 424 GLN G 643 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055333 restraints weight = 98448.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056898 restraints weight = 54784.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057900 restraints weight = 38065.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058534 restraints weight = 30370.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058929 restraints weight = 26476.197| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25896 Z= 0.202 Angle : 0.551 11.022 34959 Z= 0.309 Chirality : 0.044 0.163 4041 Planarity : 0.003 0.051 4553 Dihedral : 4.219 50.409 3277 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.47 % Allowed : 10.72 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.47 (0.14), residues: 3251 helix: -0.42 (0.25), residues: 450 sheet: 0.97 (0.18), residues: 749 loop : -0.80 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.012 0.001 TYR G 463 PHE 0.012 0.001 PHE B 618 TRP 0.004 0.001 TRP G 374 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00440 (25896) covalent geometry : angle 0.55090 (34959) hydrogen bonds : bond 0.03030 ( 711) hydrogen bonds : angle 5.44719 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7884 (tpt) cc_final: 0.7532 (tpt) REVERT: A 575 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (m) REVERT: A 608 MET cc_start: 0.9296 (mtp) cc_final: 0.8830 (mtp) REVERT: B 738 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.6771 (p) REVERT: C 451 MET cc_start: 0.6486 (ttt) cc_final: 0.5474 (ptt) REVERT: C 608 MET cc_start: 0.8554 (mtm) cc_final: 0.7924 (mtt) REVERT: C 720 ILE cc_start: 0.7716 (mm) cc_final: 0.7292 (tt) REVERT: D 451 MET cc_start: 0.5647 (tmm) cc_final: 0.5191 (tmm) REVERT: E 476 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7664 (mmmt) REVERT: E 519 ASP cc_start: 0.8695 (t0) cc_final: 0.8392 (m-30) REVERT: E 562 LEU cc_start: 0.8288 (tp) cc_final: 0.7844 (tt) REVERT: E 659 MET cc_start: 0.7829 (tmm) cc_final: 0.7462 (tmm) REVERT: E 716 ASP cc_start: 0.8284 (m-30) cc_final: 0.7995 (m-30) REVERT: F 303 MET cc_start: 0.8885 (ptm) cc_final: 0.8669 (ppp) REVERT: G 659 MET cc_start: 0.8388 (tpp) cc_final: 0.8068 (tpp) outliers start: 43 outliers final: 28 residues processed: 184 average time/residue: 0.1501 time to fit residues: 46.9954 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 256 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 83 optimal weight: 50.0000 chunk 295 optimal weight: 0.1980 chunk 282 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 192 optimal weight: 40.0000 chunk 17 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057776 restraints weight = 96409.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059484 restraints weight = 51370.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060564 restraints weight = 34735.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.061255 restraints weight = 27287.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061665 restraints weight = 23492.121| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25896 Z= 0.110 Angle : 0.500 11.677 34959 Z= 0.280 Chirality : 0.043 0.151 4041 Planarity : 0.003 0.048 4553 Dihedral : 3.769 47.196 3277 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.06 % Allowed : 11.95 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.23 (0.14), residues: 3251 helix: -0.27 (0.25), residues: 456 sheet: 1.19 (0.19), residues: 749 loop : -0.65 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.009 0.001 TYR A 260 PHE 0.010 0.001 PHE F 670 TRP 0.007 0.001 TRP F 631 HIS 0.000 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00221 (25896) covalent geometry : angle 0.49957 (34959) hydrogen bonds : bond 0.02515 ( 711) hydrogen bonds : angle 5.11869 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7935 (tpt) cc_final: 0.7634 (tpt) REVERT: A 575 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.8970 (m) REVERT: A 608 MET cc_start: 0.9278 (mtp) cc_final: 0.8782 (mtp) REVERT: B 590 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8990 (mp10) REVERT: C 451 MET cc_start: 0.6498 (ttt) cc_final: 0.5458 (ptt) REVERT: C 526 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 701 LYS cc_start: 0.8312 (tptp) cc_final: 0.7478 (mmtt) REVERT: C 720 ILE cc_start: 0.7674 (mm) cc_final: 0.7293 (tt) REVERT: D 451 MET cc_start: 0.5594 (tmm) cc_final: 0.5069 (tmm) REVERT: E 476 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7631 (mmmt) REVERT: E 519 ASP cc_start: 0.8750 (t0) cc_final: 0.8545 (m-30) REVERT: E 562 LEU cc_start: 0.8401 (tp) cc_final: 0.7989 (tt) REVERT: E 659 MET cc_start: 0.7657 (tmm) cc_final: 0.7302 (tmm) REVERT: E 716 ASP cc_start: 0.8346 (m-30) cc_final: 0.8102 (m-30) REVERT: F 303 MET cc_start: 0.8829 (ptm) cc_final: 0.8549 (ppp) REVERT: G 659 MET cc_start: 0.8514 (tpp) cc_final: 0.8301 (tpp) outliers start: 31 outliers final: 17 residues processed: 184 average time/residue: 0.1485 time to fit residues: 46.3821 Evaluate side-chains 162 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 308 optimal weight: 0.9980 chunk 172 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 318 optimal weight: 0.0670 chunk 138 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 overall best weight: 3.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057144 restraints weight = 97533.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058777 restraints weight = 53226.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059816 restraints weight = 36520.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060407 restraints weight = 28910.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060853 restraints weight = 25223.646| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25896 Z= 0.128 Angle : 0.503 12.142 34959 Z= 0.282 Chirality : 0.043 0.195 4041 Planarity : 0.003 0.046 4553 Dihedral : 3.766 45.390 3277 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.10 % Allowed : 12.12 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.19 (0.15), residues: 3251 helix: -0.23 (0.25), residues: 458 sheet: 1.25 (0.19), residues: 749 loop : -0.64 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 393 TYR 0.008 0.001 TYR A 260 PHE 0.008 0.001 PHE E 579 TRP 0.003 0.001 TRP F 244 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00269 (25896) covalent geometry : angle 0.50325 (34959) hydrogen bonds : bond 0.02512 ( 711) hydrogen bonds : angle 4.98571 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7923 (tpt) cc_final: 0.7623 (tpt) REVERT: A 575 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9027 (m) REVERT: A 608 MET cc_start: 0.9285 (mtp) cc_final: 0.8822 (mtp) REVERT: C 451 MET cc_start: 0.6551 (ttt) cc_final: 0.5551 (ptt) REVERT: C 526 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 701 LYS cc_start: 0.8325 (tptp) cc_final: 0.7890 (mmmt) REVERT: C 720 ILE cc_start: 0.7706 (mm) cc_final: 0.7306 (tt) REVERT: D 451 MET cc_start: 0.5681 (tmm) cc_final: 0.5186 (tmm) REVERT: E 562 LEU cc_start: 0.8407 (tp) cc_final: 0.8012 (tt) REVERT: E 716 ASP cc_start: 0.8287 (m-30) cc_final: 0.8018 (m-30) REVERT: F 303 MET cc_start: 0.8781 (ptm) cc_final: 0.8460 (ppp) outliers start: 32 outliers final: 22 residues processed: 169 average time/residue: 0.1537 time to fit residues: 44.0976 Evaluate side-chains 158 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 320 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 245 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 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 = 0.3510 r_free = 0.3510 target = 0.078229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055925 restraints weight = 96978.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.057503 restraints weight = 53475.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058531 restraints weight = 36976.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059164 restraints weight = 29380.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059555 restraints weight = 25551.368| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25896 Z= 0.158 Angle : 0.521 12.401 34959 Z= 0.291 Chirality : 0.044 0.161 4041 Planarity : 0.003 0.045 4553 Dihedral : 3.927 44.534 3277 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.40 % Allowed : 12.15 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.21 (0.15), residues: 3251 helix: -0.21 (0.25), residues: 457 sheet: 1.16 (0.19), residues: 766 loop : -0.64 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.009 0.001 TYR D 296 PHE 0.009 0.001 PHE B 618 TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00341 (25896) covalent geometry : angle 0.52125 (34959) hydrogen bonds : bond 0.02611 ( 711) hydrogen bonds : angle 5.00919 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7890 (tpt) cc_final: 0.7541 (tpt) REVERT: A 575 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9053 (m) REVERT: A 608 MET cc_start: 0.9305 (mtp) cc_final: 0.8836 (mtp) REVERT: B 590 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9021 (mp10) REVERT: C 451 MET cc_start: 0.6723 (ttt) cc_final: 0.5725 (ptt) REVERT: C 720 ILE cc_start: 0.7805 (mm) cc_final: 0.7381 (tt) REVERT: D 451 MET cc_start: 0.5789 (tmm) cc_final: 0.5322 (tmm) REVERT: D 523 GLN cc_start: 0.8129 (pm20) cc_final: 0.7914 (pm20) REVERT: D 697 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (tp) REVERT: E 562 LEU cc_start: 0.8427 (tp) cc_final: 0.8034 (tt) REVERT: E 659 MET cc_start: 0.7652 (tmm) cc_final: 0.7354 (tmm) REVERT: E 716 ASP cc_start: 0.8320 (m-30) cc_final: 0.8090 (m-30) REVERT: G 543 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7390 (mp0) outliers start: 41 outliers final: 27 residues processed: 168 average time/residue: 0.1522 time to fit residues: 43.7713 Evaluate side-chains 164 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 20 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 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 = 0.3491 r_free = 0.3491 target = 0.077336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055098 restraints weight = 98132.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056652 restraints weight = 54068.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057668 restraints weight = 37458.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058299 restraints weight = 29841.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058674 restraints weight = 25958.858| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25896 Z= 0.178 Angle : 0.546 13.026 34959 Z= 0.303 Chirality : 0.044 0.328 4041 Planarity : 0.003 0.045 4553 Dihedral : 4.120 44.753 3277 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.37 % Allowed : 12.60 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.30 (0.14), residues: 3251 helix: -0.25 (0.25), residues: 457 sheet: 1.13 (0.19), residues: 752 loop : -0.72 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 528 TYR 0.010 0.001 TYR D 296 PHE 0.010 0.001 PHE B 618 TRP 0.005 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00388 (25896) covalent geometry : angle 0.54603 (34959) hydrogen bonds : bond 0.02704 ( 711) hydrogen bonds : angle 5.09004 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7945 (tpt) cc_final: 0.7616 (tpt) REVERT: A 575 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9097 (m) REVERT: A 608 MET cc_start: 0.9309 (mtp) cc_final: 0.8832 (mtp) REVERT: B 590 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8990 (mp10) REVERT: C 451 MET cc_start: 0.6845 (ttt) cc_final: 0.5873 (ptt) REVERT: D 451 MET cc_start: 0.5874 (tmm) cc_final: 0.5365 (tmm) REVERT: D 697 LEU cc_start: 0.8135 (pt) cc_final: 0.7935 (tp) REVERT: E 562 LEU cc_start: 0.8436 (tp) cc_final: 0.8043 (tt) REVERT: E 659 MET cc_start: 0.7664 (tmm) cc_final: 0.7383 (tmm) REVERT: F 416 GLU cc_start: 0.7516 (pm20) cc_final: 0.7277 (pm20) REVERT: G 543 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: G 723 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8325 (p) outliers start: 40 outliers final: 32 residues processed: 171 average time/residue: 0.1511 time to fit residues: 44.2142 Evaluate side-chains 167 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 56 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 156 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054859 restraints weight = 98354.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056399 restraints weight = 54154.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057410 restraints weight = 37471.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057991 restraints weight = 29794.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058406 restraints weight = 26002.837| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25896 Z= 0.187 Angle : 0.555 14.231 34959 Z= 0.307 Chirality : 0.044 0.263 4041 Planarity : 0.003 0.045 4553 Dihedral : 4.187 45.009 3277 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.44 % Allowed : 12.87 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.36 (0.14), residues: 3251 helix: -0.24 (0.25), residues: 458 sheet: 0.96 (0.18), residues: 776 loop : -0.73 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 527 TYR 0.010 0.001 TYR D 296 PHE 0.011 0.001 PHE B 618 TRP 0.004 0.001 TRP D 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00408 (25896) covalent geometry : angle 0.55465 (34959) hydrogen bonds : bond 0.02711 ( 711) hydrogen bonds : angle 5.09943 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7960 (tpt) cc_final: 0.7625 (tpt) REVERT: A 575 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9084 (m) REVERT: A 608 MET cc_start: 0.9311 (mtp) cc_final: 0.8872 (mtp) REVERT: B 590 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8985 (mp10) REVERT: C 451 MET cc_start: 0.6852 (ttt) cc_final: 0.5952 (ptt) REVERT: C 720 ILE cc_start: 0.7987 (mm) cc_final: 0.7351 (pt) REVERT: D 451 MET cc_start: 0.5886 (tmm) cc_final: 0.5366 (tmm) REVERT: E 562 LEU cc_start: 0.8413 (tp) cc_final: 0.8030 (tt) REVERT: E 659 MET cc_start: 0.7566 (tmm) cc_final: 0.7287 (tmm) REVERT: F 303 MET cc_start: 0.9003 (ppp) cc_final: 0.8799 (ppp) REVERT: G 543 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: G 723 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8324 (p) outliers start: 42 outliers final: 34 residues processed: 162 average time/residue: 0.1490 time to fit residues: 41.9995 Evaluate side-chains 164 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 703 TYR Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 317 optimal weight: 40.0000 chunk 168 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 265 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 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 = 0.3530 r_free = 0.3530 target = 0.078867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056671 restraints weight = 97419.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058347 restraints weight = 51755.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059424 restraints weight = 35035.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060037 restraints weight = 27511.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060496 restraints weight = 23884.383| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25896 Z= 0.116 Angle : 0.519 14.710 34959 Z= 0.287 Chirality : 0.044 0.259 4041 Planarity : 0.003 0.046 4553 Dihedral : 3.845 41.940 3277 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.13 % Allowed : 13.04 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.18 (0.15), residues: 3251 helix: -0.08 (0.25), residues: 458 sheet: 1.17 (0.19), residues: 761 loop : -0.65 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.008 0.001 TYR A 260 PHE 0.009 0.001 PHE C 621 TRP 0.006 0.001 TRP F 631 HIS 0.000 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00244 (25896) covalent geometry : angle 0.51916 (34959) hydrogen bonds : bond 0.02361 ( 711) hydrogen bonds : angle 4.88295 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7957 (tpt) cc_final: 0.7664 (tpt) REVERT: A 575 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9031 (m) REVERT: A 608 MET cc_start: 0.9331 (mtp) cc_final: 0.8830 (mtp) REVERT: B 590 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8999 (mp10) REVERT: C 451 MET cc_start: 0.6859 (ttt) cc_final: 0.5942 (ptt) REVERT: C 720 ILE cc_start: 0.7981 (mm) cc_final: 0.7389 (pt) REVERT: D 451 MET cc_start: 0.5918 (tmm) cc_final: 0.5295 (tmm) REVERT: E 562 LEU cc_start: 0.8532 (tp) cc_final: 0.8156 (tt) REVERT: E 608 MET cc_start: 0.8657 (ptp) cc_final: 0.8453 (ptp) REVERT: E 659 MET cc_start: 0.7467 (tmm) cc_final: 0.7248 (tmm) REVERT: F 303 MET cc_start: 0.9032 (ppp) cc_final: 0.8822 (ppp) REVERT: F 416 GLU cc_start: 0.7623 (pm20) cc_final: 0.7399 (pm20) REVERT: G 543 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: G 723 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8321 (p) REVERT: G 739 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7861 (tm-30) outliers start: 33 outliers final: 27 residues processed: 170 average time/residue: 0.1485 time to fit residues: 43.3368 Evaluate side-chains 161 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 51 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 180 optimal weight: 0.1980 chunk 229 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 734 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 = 0.3524 r_free = 0.3524 target = 0.078635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056643 restraints weight = 96743.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058263 restraints weight = 52751.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059295 restraints weight = 36169.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059877 restraints weight = 28659.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060286 restraints weight = 24988.423| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25896 Z= 0.124 Angle : 0.527 13.927 34959 Z= 0.290 Chirality : 0.044 0.251 4041 Planarity : 0.003 0.049 4553 Dihedral : 3.815 39.798 3277 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.20 % Allowed : 13.35 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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 aren not related in a simple way. whole: -0.14 (0.15), residues: 3251 helix: -0.07 (0.25), residues: 460 sheet: 1.16 (0.18), residues: 770 loop : -0.60 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.010 0.001 TYR G 260 PHE 0.009 0.001 PHE C 621 TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00266 (25896) covalent geometry : angle 0.52690 (34959) hydrogen bonds : bond 0.02347 ( 711) hydrogen bonds : angle 4.82040 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.44 seconds wall clock time: 68 minutes 7.51 seconds (4087.51 seconds total)