Starting phenix.real_space_refine on Sat Jun 21 11:21:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsl_61776/06_2025/9jsl_61776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsl_61776/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsl_61776/06_2025/9jsl_61776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsl_61776/06_2025/9jsl_61776.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsl_61776/06_2025/9jsl_61776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsl_61776/06_2025/9jsl_61776.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.71, per 1000 atoms: 0.62 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: 5.96 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.67 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: 8.75 Time building geometry restraints manager: 7.06 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 741 or resid 901 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: 0.700 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: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 56.760 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.490 ------------------------------------------------------------------------------- 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 : 6.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP G 631 HIS 0.001 0.000 HIS E 358 PHE 0.008 0.001 PHE F 670 TYR 0.013 0.001 TYR D 296 ARG 0.000 0.000 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.25355 ( 711) hydrogen bonds : angle 9.41245 ( 1797) covalent geometry : bond 0.00250 (25896) covalent geometry : angle 0.51175 (34959) *********************** 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 : 2.934 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: 0.4566 (ptt) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.3395 time to fit residues: 175.2459 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 : 3.109 ------------------------------------------------------------------------------- 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 276 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 137 optimal weight: 0.0040 chunk 84 optimal weight: 50.0000 chunk 167 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 99 optimal weight: 0.0770 chunk 155 optimal weight: 7.9990 chunk 190 optimal weight: 40.0000 chunk 296 optimal weight: 9.9990 overall best weight: 5.2156 ------------------------------------------------------------------------------- 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 D 391 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 ASN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN G 633 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.080763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058244 restraints weight = 96342.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059956 restraints weight = 51443.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061050 restraints weight = 34816.927| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25896 Z= 0.170 Angle : 0.568 10.609 34959 Z= 0.318 Chirality : 0.045 0.169 4041 Planarity : 0.004 0.054 4553 Dihedral : 4.022 50.729 3281 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.65 % Allowed : 7.16 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3251 helix: -0.45 (0.25), residues: 455 sheet: 1.27 (0.19), residues: 734 loop : -0.70 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 631 HIS 0.001 0.000 HIS F 358 PHE 0.019 0.001 PHE C 670 TYR 0.014 0.001 TYR G 665 ARG 0.000 0.000 ARG G 289 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 711) hydrogen bonds : angle 6.17897 ( 1797) covalent geometry : bond 0.00366 (25896) covalent geometry : angle 0.56813 (34959) *********************** 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 191 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 MET cc_start: 0.9333 (mtp) cc_final: 0.8926 (mtp) REVERT: B 268 ASP cc_start: 0.8352 (p0) cc_final: 0.8141 (p0) REVERT: C 451 MET cc_start: 0.6140 (ttt) cc_final: 0.5058 (ptt) REVERT: E 364 THR cc_start: 0.7140 (p) cc_final: 0.6801 (p) REVERT: E 716 ASP cc_start: 0.8372 (m-30) cc_final: 0.8035 (m-30) REVERT: F 303 MET cc_start: 0.8966 (ptm) cc_final: 0.8355 (ppp) outliers start: 19 outliers final: 11 residues processed: 185 average time/residue: 0.4546 time to fit residues: 145.3441 Evaluate side-chains 150 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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 C residue 702 ASP 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 461 ILE 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 295 optimal weight: 5.9990 chunk 288 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 49 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 G 328 ASN ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057765 restraints weight = 96199.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059473 restraints weight = 51522.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.060559 restraints weight = 34955.774| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25896 Z= 0.142 Angle : 0.519 11.087 34959 Z= 0.292 Chirality : 0.044 0.154 4041 Planarity : 0.003 0.052 4553 Dihedral : 3.846 49.457 3277 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.82 % Allowed : 9.52 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3251 helix: -0.32 (0.25), residues: 453 sheet: 1.23 (0.19), residues: 745 loop : -0.68 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 631 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE F 670 TYR 0.013 0.001 TYR G 665 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 711) hydrogen bonds : angle 5.60080 ( 1797) covalent geometry : bond 0.00302 (25896) covalent geometry : angle 0.51852 (34959) *********************** 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 183 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 4.856 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: 0.7809 (tpt) cc_final: 0.7470 (tpt) REVERT: A 608 MET cc_start: 0.9298 (mtp) cc_final: 0.8815 (mtp) REVERT: C 451 MET cc_start: 0.6293 (ttt) cc_final: 0.5232 (ptt) REVERT: C 526 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7296 (tm-30) REVERT: C 701 LYS cc_start: 0.8236 (tptp) cc_final: 0.7401 (mmtt) REVERT: C 720 ILE cc_start: 0.7536 (mm) cc_final: 0.7187 (tt) REVERT: C 730 ILE cc_start: 0.7662 (pt) cc_final: 0.7303 (tp) REVERT: D 402 MET cc_start: 0.8561 (ttt) cc_final: 0.8320 (ttt) REVERT: E 476 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7684 (mmmt) REVERT: E 716 ASP cc_start: 0.8411 (m-30) cc_final: 0.8100 (m-30) REVERT: F 303 MET cc_start: 0.8919 (ptm) cc_final: 0.8451 (ppp) outliers start: 24 outliers final: 15 residues processed: 176 average time/residue: 0.4482 time to fit residues: 138.3110 Evaluate side-chains 155 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 488 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 740 LEU Chi-restraints excluded: chain D residue 296 TYR 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 E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain G residue 581 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 282 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 287 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 295 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 391 ASN D 431 ASN D 494 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 734 ASN ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 643 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.055805 restraints weight = 97531.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057393 restraints weight = 53870.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058416 restraints weight = 37176.601| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2596 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= 0.188 Angle : 0.546 11.226 34959 Z= 0.306 Chirality : 0.044 0.160 4041 Planarity : 0.003 0.049 4553 Dihedral : 4.115 49.573 3277 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.44 % Allowed : 10.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3251 helix: -0.40 (0.25), residues: 456 sheet: 1.06 (0.18), residues: 745 loop : -0.75 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 PHE 0.009 0.001 PHE B 618 TYR 0.012 0.001 TYR G 463 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 711) hydrogen bonds : angle 5.41484 ( 1797) covalent geometry : bond 0.00406 (25896) covalent geometry : angle 0.54568 (34959) *********************** 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 191 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9089 (m) REVERT: A 608 MET cc_start: 0.9278 (mtp) cc_final: 0.8858 (mtp) REVERT: C 451 MET cc_start: 0.6486 (ttt) cc_final: 0.5449 (ptt) REVERT: C 526 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7387 (tm-30) REVERT: C 720 ILE cc_start: 0.7606 (mm) cc_final: 0.7217 (tt) REVERT: C 730 ILE cc_start: 0.7593 (pt) cc_final: 0.7289 (tp) REVERT: D 451 MET cc_start: 0.5277 (ttt) cc_final: 0.4716 (tmm) REVERT: E 476 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7644 (mmmt) REVERT: E 659 MET cc_start: 0.7661 (tmm) cc_final: 0.7263 (tmm) REVERT: E 716 ASP cc_start: 0.8327 (m-30) cc_final: 0.8023 (m-30) REVERT: F 303 MET cc_start: 0.8807 (ptm) cc_final: 0.8485 (ppp) REVERT: F 416 GLU cc_start: 0.7676 (pm20) cc_final: 0.7445 (pm20) REVERT: G 543 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: G 659 MET cc_start: 0.8425 (tpp) cc_final: 0.8207 (tpp) outliers start: 42 outliers final: 25 residues processed: 181 average time/residue: 0.5394 time to fit residues: 172.3813 Evaluate side-chains 161 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 3.613 ------------------------------------------------------------------------------- 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 575 VAL 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 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 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 723 THR 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 543 GLU 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 6 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 322 optimal weight: 9.9990 chunk 190 optimal weight: 40.0000 chunk 229 optimal weight: 10.0000 chunk 250 optimal weight: 40.0000 chunk 129 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 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 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.077267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054972 restraints weight = 98547.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056546 restraints weight = 54548.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057561 restraints weight = 37654.832| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25896 Z= 0.203 Angle : 0.561 11.270 34959 Z= 0.313 Chirality : 0.044 0.159 4041 Planarity : 0.003 0.048 4553 Dihedral : 4.282 49.472 3277 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.68 % Allowed : 11.64 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3251 helix: -0.47 (0.25), residues: 452 sheet: 0.99 (0.19), residues: 755 loop : -0.82 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 PHE 0.011 0.001 PHE B 618 TYR 0.015 0.001 TYR G 463 ARG 0.000 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 711) hydrogen bonds : angle 5.42211 ( 1797) covalent geometry : bond 0.00443 (25896) covalent geometry : angle 0.56064 (34959) *********************** 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 191 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9075 (m) REVERT: A 608 MET cc_start: 0.9293 (mtp) cc_final: 0.8867 (mtp) REVERT: C 451 MET cc_start: 0.6594 (ttt) cc_final: 0.5605 (ptt) REVERT: C 720 ILE cc_start: 0.7696 (mm) cc_final: 0.7304 (tt) REVERT: D 451 MET cc_start: 0.5220 (ttt) cc_final: 0.4780 (tmm) REVERT: E 476 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7684 (mmmt) REVERT: E 659 MET cc_start: 0.7741 (tmm) cc_final: 0.7390 (tmm) REVERT: E 716 ASP cc_start: 0.8304 (m-30) cc_final: 0.8031 (m-30) outliers start: 49 outliers final: 32 residues processed: 182 average time/residue: 0.3248 time to fit residues: 100.6844 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 3.311 ------------------------------------------------------------------------------- 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 575 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU 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 685 VAL 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 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 684 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 392 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 161 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 42 optimal weight: 50.0000 chunk 313 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055267 restraints weight = 98366.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056838 restraints weight = 54557.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057859 restraints weight = 37807.513| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3024 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= 0.162 Angle : 0.534 11.881 34959 Z= 0.299 Chirality : 0.044 0.152 4041 Planarity : 0.003 0.046 4553 Dihedral : 4.151 48.266 3277 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.68 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3251 helix: -0.39 (0.24), residues: 458 sheet: 0.97 (0.19), residues: 764 loop : -0.80 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 PHE 0.009 0.001 PHE E 579 TYR 0.009 0.001 TYR A 260 ARG 0.000 0.000 ARG E 289 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 711) hydrogen bonds : angle 5.25149 ( 1797) covalent geometry : bond 0.00349 (25896) covalent geometry : angle 0.53448 (34959) *********************** 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 190 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9086 (m) REVERT: A 608 MET cc_start: 0.9279 (mtp) cc_final: 0.8852 (mtp) REVERT: B 590 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9014 (mp10) REVERT: C 451 MET cc_start: 0.6696 (ttt) cc_final: 0.5783 (ptt) REVERT: C 720 ILE cc_start: 0.7764 (mm) cc_final: 0.7297 (tt) REVERT: E 476 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7730 (mmmt) REVERT: E 659 MET cc_start: 0.7808 (tmm) cc_final: 0.7456 (tmm) REVERT: E 716 ASP cc_start: 0.8347 (m-30) cc_final: 0.8135 (m-30) REVERT: F 416 GLU cc_start: 0.7668 (pm20) cc_final: 0.7336 (pm20) REVERT: G 543 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7345 (mp0) outliers start: 49 outliers final: 33 residues processed: 182 average time/residue: 0.3203 time to fit residues: 101.2773 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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 575 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 586 ILE 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 685 VAL 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 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 723 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 461 ILE 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 746 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 279 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 181 optimal weight: 0.0050 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- 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 431 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055451 restraints weight = 97800.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057022 restraints weight = 53901.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058056 restraints weight = 37250.710| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3112 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= 0.152 Angle : 0.538 12.345 34959 Z= 0.299 Chirality : 0.044 0.195 4041 Planarity : 0.003 0.046 4553 Dihedral : 4.091 47.719 3277 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 13.01 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3251 helix: -0.36 (0.24), residues: 458 sheet: 0.99 (0.19), residues: 762 loop : -0.79 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 PHE 0.008 0.001 PHE B 618 TYR 0.009 0.001 TYR D 296 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02651 ( 711) hydrogen bonds : angle 5.19499 ( 1797) covalent geometry : bond 0.00327 (25896) covalent geometry : angle 0.53828 (34959) *********************** 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 175 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9086 (m) REVERT: A 608 MET cc_start: 0.9282 (mtp) cc_final: 0.8851 (mtp) REVERT: B 586 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 590 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8948 (mp10) REVERT: C 720 ILE cc_start: 0.7824 (mm) cc_final: 0.7354 (tt) REVERT: D 451 MET cc_start: 0.5464 (tmm) cc_final: 0.4946 (tmm) REVERT: D 697 LEU cc_start: 0.8186 (pt) cc_final: 0.7985 (tp) REVERT: E 476 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7701 (mmmt) REVERT: E 659 MET cc_start: 0.7689 (tmm) cc_final: 0.7355 (tmm) REVERT: G 543 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7335 (mp0) outliers start: 43 outliers final: 30 residues processed: 167 average time/residue: 0.3879 time to fit residues: 112.3559 Evaluate side-chains 160 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 4.313 ------------------------------------------------------------------------------- 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 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 586 ILE 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 685 VAL 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 562 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 723 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR 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 746 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 172 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 317 optimal weight: 40.0000 chunk 90 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 218 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055517 restraints weight = 97072.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057079 restraints weight = 53553.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058108 restraints weight = 37031.899| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3180 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= 0.149 Angle : 0.539 13.093 34959 Z= 0.299 Chirality : 0.044 0.313 4041 Planarity : 0.003 0.054 4553 Dihedral : 4.048 47.014 3277 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.64 % Allowed : 13.04 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3251 helix: -0.31 (0.25), residues: 458 sheet: 0.99 (0.19), residues: 769 loop : -0.78 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 PHE 0.008 0.001 PHE E 579 TYR 0.009 0.001 TYR D 296 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.02610 ( 711) hydrogen bonds : angle 5.11710 ( 1797) covalent geometry : bond 0.00321 (25896) covalent geometry : angle 0.53873 (34959) *********************** 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 180 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9081 (m) REVERT: A 608 MET cc_start: 0.9282 (mtp) cc_final: 0.8853 (mtp) REVERT: B 586 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 590 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8952 (mp10) REVERT: C 451 MET cc_start: 0.6804 (ttt) cc_final: 0.5870 (ptt) REVERT: D 451 MET cc_start: 0.5635 (tmm) cc_final: 0.5095 (tmm) REVERT: D 697 LEU cc_start: 0.8247 (pt) cc_final: 0.8032 (tp) REVERT: E 476 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7758 (mmmt) REVERT: E 659 MET cc_start: 0.7675 (tmm) cc_final: 0.7367 (tmm) REVERT: F 416 GLU cc_start: 0.7639 (pm20) cc_final: 0.6697 (pm20) REVERT: G 543 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7361 (mp0) outliers start: 48 outliers final: 34 residues processed: 173 average time/residue: 0.3191 time to fit residues: 95.4370 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 586 ILE 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 685 VAL 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 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 338 VAL 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 723 THR 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 463 TYR 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 746 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 504 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055625 restraints weight = 97548.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057205 restraints weight = 53690.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058239 restraints weight = 37030.777| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3241 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 : 0.537 13.572 34959 Z= 0.297 Chirality : 0.044 0.265 4041 Planarity : 0.003 0.058 4553 Dihedral : 4.003 45.611 3277 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.40 % Allowed : 13.35 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3251 helix: -0.26 (0.25), residues: 457 sheet: 1.01 (0.18), residues: 769 loop : -0.75 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 PHE 0.009 0.001 PHE E 579 TYR 0.009 0.001 TYR D 296 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.02544 ( 711) hydrogen bonds : angle 5.04874 ( 1797) covalent geometry : bond 0.00305 (25896) covalent geometry : angle 0.53713 (34959) *********************** 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 172 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9079 (m) REVERT: A 608 MET cc_start: 0.9280 (mtp) cc_final: 0.8852 (mtp) REVERT: B 586 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 590 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: C 451 MET cc_start: 0.6868 (ttt) cc_final: 0.5947 (ptt) REVERT: C 720 ILE cc_start: 0.7868 (mm) cc_final: 0.7320 (pt) REVERT: C 722 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 451 MET cc_start: 0.5698 (tmm) cc_final: 0.5256 (tmm) REVERT: E 476 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7750 (mmmt) REVERT: E 659 MET cc_start: 0.7679 (tmm) cc_final: 0.7388 (tmm) REVERT: F 303 MET cc_start: 0.8871 (ppp) cc_final: 0.8629 (ppp) REVERT: F 416 GLU cc_start: 0.7649 (pm20) cc_final: 0.7384 (pm20) REVERT: G 543 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: G 723 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8362 (p) outliers start: 41 outliers final: 34 residues processed: 164 average time/residue: 0.3092 time to fit residues: 87.6532 Evaluate side-chains 169 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 586 ILE 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 685 VAL Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 722 ILE 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 619 THR Chi-restraints excluded: chain E residue 338 VAL 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 723 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 703 TYR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR 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 737 ILE 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 62 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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** C 681 ASN F 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054106 restraints weight = 98361.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055648 restraints weight = 54590.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056655 restraints weight = 37804.888| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25896 Z= 0.228 Angle : 0.597 12.843 34959 Z= 0.329 Chirality : 0.045 0.256 4041 Planarity : 0.004 0.060 4553 Dihedral : 4.423 47.277 3277 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.47 % Allowed : 13.49 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3251 helix: -0.41 (0.24), residues: 460 sheet: 0.81 (0.18), residues: 774 loop : -0.88 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 631 HIS 0.001 0.001 HIS F 358 PHE 0.013 0.001 PHE B 618 TYR 0.013 0.001 TYR D 296 ARG 0.000 0.000 ARG D 527 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 711) hydrogen bonds : angle 5.25358 ( 1797) covalent geometry : bond 0.00501 (25896) covalent geometry : angle 0.59713 (34959) ********************** 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 166 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9083 (m) REVERT: A 608 MET cc_start: 0.9340 (mtp) cc_final: 0.8925 (mtp) REVERT: C 720 ILE cc_start: 0.7862 (mm) cc_final: 0.7232 (pt) REVERT: C 722 ILE cc_start: 0.8501 (mt) cc_final: 0.8249 (mm) REVERT: D 451 MET cc_start: 0.5772 (tmm) cc_final: 0.5330 (tmm) REVERT: E 476 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7886 (mmmt) REVERT: E 608 MET cc_start: 0.8634 (ptp) cc_final: 0.8408 (ptp) REVERT: E 659 MET cc_start: 0.7722 (tmm) cc_final: 0.7431 (tmm) REVERT: F 303 MET cc_start: 0.8959 (ppp) cc_final: 0.8504 (ppp) REVERT: F 416 GLU cc_start: 0.7529 (pm20) cc_final: 0.7234 (pm20) REVERT: G 543 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: G 723 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8382 (p) outliers start: 43 outliers final: 34 residues processed: 158 average time/residue: 0.3250 time to fit residues: 89.4059 Evaluate side-chains 157 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 3.018 ------------------------------------------------------------------------------- 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 645 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR 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 685 VAL 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 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 338 VAL 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 723 THR Chi-restraints excluded: chain F residue 703 TYR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR 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 247 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 76 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055845 restraints weight = 97537.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057444 restraints weight = 53405.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058474 restraints weight = 36764.688| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3379 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= 0.123 Angle : 0.537 13.457 34959 Z= 0.296 Chirality : 0.044 0.254 4041 Planarity : 0.003 0.061 4553 Dihedral : 4.018 44.699 3277 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.23 % Allowed : 13.63 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3251 helix: -0.19 (0.25), residues: 457 sheet: 0.97 (0.18), residues: 763 loop : -0.77 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 631 HIS 0.000 0.000 HIS E 358 PHE 0.009 0.001 PHE C 621 TYR 0.008 0.001 TYR A 260 ARG 0.000 0.000 ARG G 324 Details of bonding type rmsd hydrogen bonds : bond 0.02463 ( 711) hydrogen bonds : angle 5.01677 ( 1797) covalent geometry : bond 0.00260 (25896) covalent geometry : angle 0.53660 (34959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7859.45 seconds wall clock time: 142 minutes 37.92 seconds (8557.92 seconds total)