Starting phenix.real_space_refine on Sun Jul 5 01:38:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsl_61776/07_2026/9jsl_61776.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 39 5.16 5 C 16181 2.51 5 N 4063 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25496 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3488 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3481 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 429} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3830 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3836 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3852 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 5.21, per 1000 atoms: 0.20 Number of scatterers: 25496 At special positions: 0 Unit cell: (176.88, 176, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 39 16.00 O 5192 8.00 N 4063 7.00 C 16181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 867.8 milliseconds 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: 0.89 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: 4.63 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4588 1.28 - 1.41: 5557 1.41 - 1.55: 15661 1.55 - 1.68: 19 1.68 - 1.81: 71 Bond restraints: 25896 Sorted by residual: bond pdb=" C GLU G 548 " pdb=" O GLU G 548 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.16e-02 7.43e+03 5.50e+01 bond pdb=" C GLU G 548 " pdb=" N ALA G 549 " ideal model delta sigma weight residual 1.335 1.268 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C GLY G 547 " pdb=" N GLU G 548 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.33e-02 5.65e+03 1.31e+01 bond pdb=" CA GLU G 548 " pdb=" C GLU G 548 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.26e-02 6.30e+03 5.10e+00 bond pdb=" CD2 TRP E 374 " pdb=" CE2 TRP E 374 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.87e+00 ... (remaining 25891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 34361 1.65 - 3.31: 512 3.31 - 4.96: 63 4.96 - 6.61: 18 6.61 - 8.26: 5 Bond angle restraints: 34959 Sorted by residual: angle pdb=" N GLU G 548 " pdb=" CA GLU G 548 " pdb=" C GLU G 548 " ideal model delta sigma weight residual 111.14 103.71 7.43 1.08e+00 8.57e-01 4.73e+01 angle pdb=" C GLU G 548 " pdb=" CA GLU G 548 " pdb=" CB GLU G 548 " ideal model delta sigma weight residual 110.90 118.45 -7.55 1.58e+00 4.01e-01 2.29e+01 angle pdb=" N VAL D 512 " pdb=" CA VAL D 512 " pdb=" C VAL D 512 " ideal model delta sigma weight residual 113.20 108.87 4.33 9.60e-01 1.09e+00 2.03e+01 angle pdb=" CD2 TRP F 374 " pdb=" CE3 TRP F 374 " pdb=" CZ3 TRP F 374 " ideal model delta sigma weight residual 118.60 124.00 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CD2 TRP B 631 " pdb=" CE3 TRP B 631 " pdb=" CZ3 TRP B 631 " ideal model delta sigma weight residual 118.60 123.98 -5.38 1.30e+00 5.92e-01 1.71e+01 ... (remaining 34954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14181 17.96 - 35.92: 1257 35.92 - 53.88: 213 53.88 - 71.83: 45 71.83 - 89.79: 29 Dihedral angle restraints: 15725 sinusoidal: 6252 harmonic: 9473 Sorted by residual: dihedral pdb=" CA ILE C 459 " pdb=" C ILE C 459 " pdb=" N PRO C 460 " pdb=" CA PRO C 460 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB GLU G 700 " pdb=" CG GLU G 700 " pdb=" CD GLU G 700 " pdb=" OE1 GLU G 700 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU F 691 " pdb=" CG GLU F 691 " pdb=" CD GLU F 691 " pdb=" OE1 GLU F 691 " ideal model delta sinusoidal sigma weight residual 0.00 -89.37 89.37 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2613 0.033 - 0.066: 904 0.066 - 0.099: 307 0.099 - 0.133: 209 0.133 - 0.166: 8 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CA GLU G 548 " pdb=" N GLU G 548 " pdb=" C GLU G 548 " pdb=" CB GLU G 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB ILE D 657 " pdb=" CA ILE D 657 " pdb=" CG1 ILE D 657 " pdb=" CG2 ILE D 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE A 657 " pdb=" CA ILE A 657 " pdb=" CG1 ILE A 657 " pdb=" CG2 ILE A 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 4038 not shown) Planarity restraints: 4553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 548 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLU G 548 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU G 548 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA G 549 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO D 269 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 698 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO F 699 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 699 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 699 " -0.033 5.00e-02 4.00e+02 ... (remaining 4550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3514 2.76 - 3.29: 24135 3.29 - 3.83: 39974 3.83 - 4.36: 47271 4.36 - 4.90: 84270 Nonbonded interactions: 199164 Sorted by model distance: nonbonded pdb=" O LYS G 468 " pdb=" OG SER G 471 " model vdw 2.224 3.040 nonbonded pdb=" OG SER C 259 " pdb=" OE1 GLU C 262 " model vdw 2.228 3.040 nonbonded pdb=" O ASP C 581 " pdb=" OG SER C 584 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU B 287 " pdb=" NE ARG B 527 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU E 572 " pdb=" NZ LYS E 598 " model vdw 2.255 3.120 ... (remaining 199159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 903)) selection = (chain 'B' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'C' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'D' and (resid 216 through 308 or resid 386 or resid 388 through 449 or r \ esid 460 through 741 or resid 901 through 903)) selection = (chain 'E' and (resid 216 through 308 or resid 342 or resid 388 through 449 or r \ esid 460 through 614 or (resid 615 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 616 through 741 or resid 901 through 903)) selection = (chain 'F' and (resid 216 through 307 or resid 340 or resid 365 or resid 380 thr \ ough 449 or resid 460 through 614 or (resid 615 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 616 through 741 or resid 901 throug \ h 903)) selection = (chain 'G' and (resid 216 through 308 or resid 365 or resid 380 through 381 or r \ esid 390 through 449 or resid 460 through 614 or (resid 615 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 616 through 741 or resi \ d 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 25896 Z= 0.138 Angle : 0.512 8.263 34959 Z= 0.304 Chirality : 0.043 0.166 4041 Planarity : 0.004 0.060 4553 Dihedral : 14.393 89.793 9527 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.14 % Allowed : 0.48 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3251 helix: -0.83 (0.24), residues: 454 sheet: 1.42 (0.20), residues: 726 loop : -0.73 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 606 TYR 0.013 0.001 TYR D 296 PHE 0.008 0.001 PHE F 670 TRP 0.005 0.001 TRP G 631 HIS 0.001 0.000 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (25896) covalent geometry : angle 0.51175 / 0.30 (34959) hydrogen bonds : bond 0.25355 / 15.96 ( 711) hydrogen bonds : angle 9.41245 / 6.42 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.4870 (ttt) cc_final: 0.4569 (ptt) outliers start: 4 outliers final: 3 residues processed: 318 average time/residue: 0.1584 time to fit residues: 82.4229 Evaluate side-chains 172 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain D residue 296 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 30.0000 overall best weight: 3.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 ASN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 734 ASN C 638 ASN D 391 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 ASN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN G 523 GLN G 633 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.059410 restraints weight = 95250.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061158 restraints weight = 50402.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062262 restraints weight = 33889.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062957 restraints weight = 26534.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063378 restraints weight = 22831.587| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1654 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= 0.149 Angle : 0.556 10.437 34959 Z= 0.313 Chirality : 0.045 0.171 4041 Planarity : 0.004 0.054 4553 Dihedral : 3.922 50.246 3281 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.58 % Allowed : 7.05 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3251 helix: -0.39 (0.25), residues: 458 sheet: 1.37 (0.19), residues: 731 loop : -0.67 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 324 TYR 0.016 0.001 TYR G 665 PHE 0.019 0.001 PHE C 670 TRP 0.006 0.001 TRP G 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (25896) covalent geometry : angle 0.55621 / 0.31 (34959) hydrogen bonds : bond 0.03903 / 2.53 ( 711) hydrogen bonds : angle 6.25840 / 4.31 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.112 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 608 MET cc_start: 0.9340 (mtp) cc_final: 0.8920 (mtp) REVERT: C 451 MET cc_start: 0.6107 (ttt) cc_final: 0.5013 (ptt) REVERT: C 627 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: E 476 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7535 (mmmt) REVERT: F 303 MET cc_start: 0.8943 (ptm) cc_final: 0.8373 (ppp) REVERT: G 608 MET cc_start: 0.9000 (mtp) cc_final: 0.8466 (mtp) outliers start: 17 outliers final: 7 residues processed: 183 average time/residue: 0.1481 time to fit residues: 45.6559 Evaluate side-chains 152 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain D residue 296 TYR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 309 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN G 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057689 restraints weight = 96155.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.059386 restraints weight = 51239.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060473 restraints weight = 34623.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061149 restraints weight = 27174.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.061532 restraints weight = 23448.698| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2195 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= 0.156 Angle : 0.522 11.121 34959 Z= 0.295 Chirality : 0.044 0.156 4041 Planarity : 0.004 0.052 4553 Dihedral : 3.896 49.666 3277 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.82 % Allowed : 9.45 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3251 helix: -0.23 (0.25), residues: 454 sheet: 1.25 (0.19), residues: 743 loop : -0.67 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 324 TYR 0.012 0.001 TYR G 665 PHE 0.009 0.001 PHE F 670 TRP 0.003 0.001 TRP F 244 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (25896) covalent geometry : angle 0.52211 / 0.29 (34959) hydrogen bonds : bond 0.03210 / 2.08 ( 711) hydrogen bonds : angle 5.57004 / 3.84 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7829 (tpt) cc_final: 0.7480 (tpt) REVERT: A 608 MET cc_start: 0.9313 (mtp) cc_final: 0.8836 (mtp) REVERT: C 451 MET cc_start: 0.6295 (ttt) cc_final: 0.5209 (ptt) REVERT: C 720 ILE cc_start: 0.7463 (mm) cc_final: 0.7109 (tt) REVERT: D 402 MET cc_start: 0.8602 (ttt) cc_final: 0.8382 (ttt) REVERT: E 476 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7662 (mmmt) REVERT: E 716 ASP cc_start: 0.8308 (m-30) cc_final: 0.7991 (m-30) REVERT: F 303 MET cc_start: 0.8937 (ptm) cc_final: 0.8474 (ppp) outliers start: 24 outliers final: 19 residues processed: 172 average time/residue: 0.1540 time to fit residues: 44.9850 Evaluate side-chains 159 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 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 F residue 424 GLN Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 189 optimal weight: 40.0000 chunk 117 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN D 431 ASN D 494 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN G 643 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.055582 restraints weight = 96905.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057145 restraints weight = 53675.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058159 restraints weight = 37147.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058784 restraints weight = 29528.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.059150 restraints weight = 25684.831| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25896 Z= 0.217 Angle : 0.563 11.989 34959 Z= 0.315 Chirality : 0.045 0.172 4041 Planarity : 0.004 0.049 4553 Dihedral : 4.233 50.331 3277 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.51 % Allowed : 10.51 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3251 helix: -0.34 (0.25), residues: 457 sheet: 1.00 (0.18), residues: 746 loop : -0.81 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 289 TYR 0.012 0.001 TYR D 296 PHE 0.011 0.001 PHE B 618 TRP 0.006 0.001 TRP C 631 HIS 0.002 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (25896) covalent geometry : angle 0.56314 / 0.31 (34959) hydrogen bonds : bond 0.03158 / 2.05 ( 711) hydrogen bonds : angle 5.49982 / 3.81 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.128 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: 0.9364 (OUTLIER) cc_final: 0.9101 (m) REVERT: A 608 MET cc_start: 0.9315 (mtp) cc_final: 0.8865 (mtp) REVERT: C 451 MET cc_start: 0.6505 (ttt) cc_final: 0.5497 (ptt) REVERT: C 720 ILE cc_start: 0.7668 (mm) cc_final: 0.7249 (tt) REVERT: D 451 MET cc_start: 0.5273 (ttt) cc_final: 0.4738 (tmm) REVERT: E 476 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7625 (mmmt) REVERT: E 659 MET cc_start: 0.7859 (tmm) cc_final: 0.7474 (tmm) REVERT: E 716 ASP cc_start: 0.8266 (m-30) cc_final: 0.7969 (m-30) REVERT: F 303 MET cc_start: 0.8833 (ptm) cc_final: 0.8492 (ppp) REVERT: G 543 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: G 659 MET cc_start: 0.8068 (tpp) cc_final: 0.7767 (tpp) outliers start: 44 outliers final: 28 residues processed: 183 average time/residue: 0.1522 time to fit residues: 47.2425 Evaluate side-chains 164 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 SER 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 495 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 702 ASP Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 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 594 LEU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 645 VAL Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 364 THR 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 746 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 256 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 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 = 0.3532 r_free = 0.3532 target = 0.079383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.056803 restraints weight = 95938.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058477 restraints weight = 51681.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059546 restraints weight = 35129.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.060209 restraints weight = 27688.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060613 restraints weight = 23955.923| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2729 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= 0.126 Angle : 0.510 11.853 34959 Z= 0.286 Chirality : 0.044 0.158 4041 Planarity : 0.003 0.047 4553 Dihedral : 3.946 48.580 3277 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.16 % Allowed : 12.02 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3251 helix: -0.28 (0.25), residues: 458 sheet: 1.15 (0.19), residues: 751 loop : -0.71 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.011 0.001 TYR A 260 PHE 0.009 0.001 PHE F 670 TRP 0.005 0.001 TRP F 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (25896) covalent geometry : angle 0.51039 / 0.29 (34959) hydrogen bonds : bond 0.02683 / 1.74 ( 711) hydrogen bonds : angle 5.25532 / 3.62 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9019 (m) REVERT: A 608 MET cc_start: 0.9330 (mtp) cc_final: 0.8798 (mtp) REVERT: C 451 MET cc_start: 0.6506 (ttt) cc_final: 0.5441 (ptt) REVERT: C 526 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 720 ILE cc_start: 0.7719 (mm) cc_final: 0.7326 (tt) REVERT: D 451 MET cc_start: 0.5262 (ttt) cc_final: 0.4804 (tmm) REVERT: D 523 GLN cc_start: 0.8416 (pm20) cc_final: 0.8207 (pm20) REVERT: E 476 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7695 (mmmt) REVERT: E 659 MET cc_start: 0.7672 (tmm) cc_final: 0.7310 (tmm) REVERT: E 716 ASP cc_start: 0.8372 (m-30) cc_final: 0.8132 (m-30) REVERT: F 303 MET cc_start: 0.8937 (ptm) cc_final: 0.8485 (ppp) REVERT: F 416 GLU cc_start: 0.7650 (pm20) cc_final: 0.7413 (pm20) REVERT: G 543 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: G 659 MET cc_start: 0.7983 (tpp) cc_final: 0.7592 (tpp) outliers start: 34 outliers final: 24 residues processed: 176 average time/residue: 0.1444 time to fit residues: 43.4688 Evaluate side-chains 162 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 B residue 586 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 645 VAL 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 D residue 296 TYR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 684 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 308 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 138 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 187 optimal weight: 6.9990 overall best weight: 4.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 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 = 0.3519 r_free = 0.3519 target = 0.078713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.056245 restraints weight = 96738.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057902 restraints weight = 52134.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058957 restraints weight = 35491.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059622 restraints weight = 27941.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060044 restraints weight = 24145.077| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2878 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= 0.143 Angle : 0.513 12.034 34959 Z= 0.286 Chirality : 0.044 0.153 4041 Planarity : 0.003 0.045 4553 Dihedral : 3.927 47.398 3277 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.44 % Allowed : 12.15 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3251 helix: -0.18 (0.25), residues: 458 sheet: 1.17 (0.19), residues: 763 loop : -0.71 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 457 TYR 0.010 0.001 TYR A 260 PHE 0.008 0.001 PHE E 579 TRP 0.004 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (25896) covalent geometry : angle 0.51258 / 0.29 (34959) hydrogen bonds : bond 0.02697 / 1.76 ( 711) hydrogen bonds : angle 5.10440 / 3.51 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9049 (m) REVERT: A 608 MET cc_start: 0.9327 (mtp) cc_final: 0.8819 (mtp) REVERT: B 590 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9009 (mp10) REVERT: C 451 MET cc_start: 0.6521 (ttt) cc_final: 0.5512 (ptt) REVERT: C 526 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 720 ILE cc_start: 0.7826 (mm) cc_final: 0.7394 (tt) REVERT: D 451 MET cc_start: 0.5404 (ttt) cc_final: 0.5166 (tmm) REVERT: D 523 GLN cc_start: 0.8423 (pm20) cc_final: 0.8061 (pm20) REVERT: E 476 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7778 (mmmt) REVERT: E 562 LEU cc_start: 0.8459 (tp) cc_final: 0.8057 (tt) REVERT: E 659 MET cc_start: 0.7675 (tmm) cc_final: 0.7328 (tmm) REVERT: E 716 ASP cc_start: 0.8342 (m-30) cc_final: 0.8098 (m-30) REVERT: F 303 MET cc_start: 0.8920 (ptm) cc_final: 0.8481 (ppp) REVERT: G 543 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: G 659 MET cc_start: 0.8063 (tpp) cc_final: 0.7745 (tpp) outliers start: 42 outliers final: 29 residues processed: 182 average time/residue: 0.1432 time to fit residues: 44.5109 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 495 ILE 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 645 VAL 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 E residue 227 ASP Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 320 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054731 restraints weight = 97021.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.056281 restraints weight = 53866.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.057285 restraints weight = 37283.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057923 restraints weight = 29658.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058259 restraints weight = 25734.058| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25896 Z= 0.222 Angle : 0.574 12.083 34959 Z= 0.318 Chirality : 0.045 0.176 4041 Planarity : 0.003 0.044 4553 Dihedral : 4.346 49.233 3277 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.64 % Allowed : 12.56 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3251 helix: -0.31 (0.25), residues: 459 sheet: 0.95 (0.18), residues: 773 loop : -0.82 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.012 0.001 TYR D 296 PHE 0.012 0.001 PHE B 618 TRP 0.006 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (25896) covalent geometry : angle 0.57444 / 0.32 (34959) hydrogen bonds : bond 0.03010 / 1.97 ( 711) hydrogen bonds : angle 5.31662 / 3.66 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9089 (m) REVERT: A 608 MET cc_start: 0.9346 (mtp) cc_final: 0.8883 (mtp) REVERT: C 526 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 451 MET cc_start: 0.5530 (ttt) cc_final: 0.5305 (tmm) REVERT: D 523 GLN cc_start: 0.8470 (pm20) cc_final: 0.8234 (pm20) REVERT: E 476 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7738 (mmmt) REVERT: E 562 LEU cc_start: 0.8392 (tp) cc_final: 0.7991 (tt) REVERT: E 659 MET cc_start: 0.7740 (tmm) cc_final: 0.7387 (tmm) REVERT: G 543 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: G 659 MET cc_start: 0.8044 (tpp) cc_final: 0.7674 (tpp) outliers start: 48 outliers final: 34 residues processed: 174 average time/residue: 0.1366 time to fit residues: 40.8790 Evaluate side-chains 166 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 645 VAL 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 475 ILE Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 619 THR Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 20 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 110 optimal weight: 0.0000 chunk 29 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 50.0000 chunk 100 optimal weight: 8.9990 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3505 r_free = 0.3505 target = 0.077970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055630 restraints weight = 96669.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057266 restraints weight = 52011.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058326 restraints weight = 35438.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058937 restraints weight = 27898.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059389 restraints weight = 24201.726| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3171 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 : 0.535 12.863 34959 Z= 0.296 Chirality : 0.044 0.153 4041 Planarity : 0.003 0.044 4553 Dihedral : 4.098 47.910 3277 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.51 % Allowed : 12.74 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3251 helix: -0.18 (0.25), residues: 458 sheet: 1.01 (0.19), residues: 767 loop : -0.75 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 528 TYR 0.011 0.001 TYR E 260 PHE 0.009 0.001 PHE C 621 TRP 0.005 0.001 TRP A 244 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (25896) covalent geometry : angle 0.53525 / 0.30 (34959) hydrogen bonds : bond 0.02673 / 1.75 ( 711) hydrogen bonds : angle 5.12282 / 3.51 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9055 (m) REVERT: A 608 MET cc_start: 0.9340 (mtp) cc_final: 0.8803 (mtp) REVERT: B 586 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (tt) REVERT: B 590 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8958 (mp10) REVERT: C 526 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 720 ILE cc_start: 0.8006 (mm) cc_final: 0.7434 (pt) REVERT: D 303 MET cc_start: 0.8250 (mmm) cc_final: 0.7897 (tmm) REVERT: D 451 MET cc_start: 0.5497 (ttt) cc_final: 0.5010 (tmm) REVERT: D 523 GLN cc_start: 0.8453 (pm20) cc_final: 0.8065 (pm20) REVERT: E 476 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7770 (mmmt) REVERT: E 562 LEU cc_start: 0.8485 (tp) cc_final: 0.8082 (tt) REVERT: E 659 MET cc_start: 0.7535 (tmm) cc_final: 0.7251 (tmm) REVERT: F 303 MET cc_start: 0.8952 (ppp) cc_final: 0.8612 (ppp) REVERT: F 416 GLU cc_start: 0.7511 (pm20) cc_final: 0.7256 (pm20) REVERT: G 543 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: G 659 MET cc_start: 0.7965 (tpp) cc_final: 0.7621 (tpp) REVERT: G 723 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8399 (p) outliers start: 44 outliers final: 31 residues processed: 175 average time/residue: 0.1505 time to fit residues: 45.2102 Evaluate side-chains 167 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 495 ILE 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 645 VAL 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 736 SER Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 56 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 178 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054907 restraints weight = 96804.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056531 restraints weight = 52330.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057581 restraints weight = 35721.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058230 restraints weight = 28182.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058595 restraints weight = 24387.778| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3281 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= 0.176 Angle : 0.552 13.361 34959 Z= 0.305 Chirality : 0.044 0.156 4041 Planarity : 0.003 0.044 4553 Dihedral : 4.173 47.976 3277 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.44 % Allowed : 13.01 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3251 helix: -0.20 (0.25), residues: 459 sheet: 0.96 (0.18), residues: 773 loop : -0.78 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 393 TYR 0.011 0.001 TYR E 260 PHE 0.010 0.001 PHE B 618 TRP 0.004 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (25896) covalent geometry : angle 0.55158 / 0.31 (34959) hydrogen bonds : bond 0.02802 / 1.84 ( 711) hydrogen bonds : angle 5.15773 / 3.53 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9041 (m) REVERT: A 608 MET cc_start: 0.9365 (mtp) cc_final: 0.8838 (mtp) REVERT: B 586 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 590 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8946 (mp10) REVERT: C 526 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 720 ILE cc_start: 0.7960 (mm) cc_final: 0.7351 (pt) REVERT: D 451 MET cc_start: 0.5558 (ttt) cc_final: 0.5067 (tmm) REVERT: D 523 GLN cc_start: 0.8440 (pm20) cc_final: 0.8048 (pm20) REVERT: E 476 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7855 (mmmt) REVERT: E 562 LEU cc_start: 0.8497 (tp) cc_final: 0.8095 (tt) REVERT: E 659 MET cc_start: 0.7630 (tmm) cc_final: 0.7364 (tmm) REVERT: F 303 MET cc_start: 0.9025 (ppp) cc_final: 0.8809 (ppp) REVERT: F 416 GLU cc_start: 0.7573 (pm20) cc_final: 0.7330 (pm20) REVERT: G 543 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: G 659 MET cc_start: 0.7967 (tpp) cc_final: 0.7590 (tpp) REVERT: G 723 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (p) outliers start: 42 outliers final: 36 residues processed: 159 average time/residue: 0.1461 time to fit residues: 40.2549 Evaluate side-chains 164 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 650 SER Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 495 ILE 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 645 VAL 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 698 VAL Chi-restraints excluded: chain E residue 736 SER Chi-restraints excluded: chain F residue 427 GLN Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain G residue 258 SER 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 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 233 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 168 optimal weight: 0.0570 chunk 4 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 35 optimal weight: 50.0000 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3522 r_free = 0.3522 target = 0.078691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056320 restraints weight = 96323.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057980 restraints weight = 51688.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059048 restraints weight = 35161.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059732 restraints weight = 27652.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060095 restraints weight = 23823.405| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25896 Z= 0.123 Angle : 0.525 13.898 34959 Z= 0.290 Chirality : 0.044 0.149 4041 Planarity : 0.003 0.050 4553 Dihedral : 3.910 45.900 3277 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.16 % Allowed : 13.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3251 helix: -0.06 (0.25), residues: 459 sheet: 1.13 (0.18), residues: 773 loop : -0.69 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 528 TYR 0.010 0.001 TYR A 260 PHE 0.010 0.001 PHE C 621 TRP 0.005 0.001 TRP G 631 HIS 0.000 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (25896) covalent geometry : angle 0.52513 / 0.29 (34959) hydrogen bonds : bond 0.02550 / 1.68 ( 711) hydrogen bonds : angle 4.96742 / 3.39 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9032 (m) REVERT: A 608 MET cc_start: 0.9336 (mtp) cc_final: 0.8788 (mtp) REVERT: B 590 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8938 (mp10) REVERT: C 526 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 722 ILE cc_start: 0.8527 (mt) cc_final: 0.8289 (mm) REVERT: D 451 MET cc_start: 0.5379 (ttt) cc_final: 0.4815 (tmm) REVERT: D 523 GLN cc_start: 0.8413 (pm20) cc_final: 0.8145 (pm20) REVERT: E 476 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7776 (mmmt) REVERT: E 562 LEU cc_start: 0.8432 (tp) cc_final: 0.8025 (tt) REVERT: E 659 MET cc_start: 0.7618 (tmm) cc_final: 0.7379 (tmm) REVERT: F 303 MET cc_start: 0.9010 (ppp) cc_final: 0.8799 (ppp) REVERT: F 416 GLU cc_start: 0.7630 (pm20) cc_final: 0.7423 (pm20) REVERT: F 683 ILE cc_start: 0.8790 (mm) cc_final: 0.8546 (mm) REVERT: G 543 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: G 659 MET cc_start: 0.7930 (tpp) cc_final: 0.7630 (tpp) REVERT: G 723 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8373 (p) REVERT: G 739 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 34 outliers final: 28 residues processed: 166 average time/residue: 0.1435 time to fit residues: 40.8221 Evaluate side-chains 165 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 645 VAL 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 562 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain E residue 227 ASP 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 G residue 258 SER 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 464 ASP Chi-restraints excluded: chain G residue 543 GLU Chi-restraints excluded: chain G residue 581 ASP Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 746 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055436 restraints weight = 95985.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057063 restraints weight = 51812.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058112 restraints weight = 35250.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058708 restraints weight = 27748.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.059143 restraints weight = 24125.801| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25896 Z= 0.156 Angle : 0.542 13.338 34959 Z= 0.298 Chirality : 0.044 0.152 4041 Planarity : 0.003 0.057 4553 Dihedral : 3.997 45.515 3277 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.34 % Allowed : 13.28 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3251 helix: -0.06 (0.25), residues: 459 sheet: 0.99 (0.18), residues: 769 loop : -0.70 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 393 TYR 0.010 0.001 TYR A 260 PHE 0.010 0.001 PHE C 621 TRP 0.005 0.001 TRP C 631 HIS 0.001 0.000 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (25896) covalent geometry : angle 0.54160 / 0.30 (34959) hydrogen bonds : bond 0.02684 / 1.77 ( 711) hydrogen bonds : angle 4.98044 / 3.40 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.72 seconds wall clock time: 66 minutes 57.93 seconds (4017.93 seconds total)