Starting phenix.real_space_refine on Sat Jun 21 00:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsn_61778/06_2025/9jsn_61778.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.083 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 41 5.16 5 C 15792 2.51 5 N 3946 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24834 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" 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: "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: 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: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3486 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: "F" 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: "G" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3857 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.59, per 1000 atoms: 0.55 Number of scatterers: 24834 At special positions: 0 Unit cell: (176.88, 176, 95.92, 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 41 16.00 O 5034 8.00 N 3946 7.00 C 15792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 3.0 seconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 63 sheets defined 18.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.526A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.738A 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 290 removed outlier: 3.917A pdb=" N ASP A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.109A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.760A pdb=" N LYS A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.847A pdb=" N ASN A 504 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.734A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.869A 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 'B' and resid 226 through 232 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.862A 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 290 removed outlier: 3.906A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 4.157A pdb=" N ILE B 428 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.807A pdb=" N LYS B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 504 removed outlier: 3.825A pdb=" N ASN B 504 " --> pdb=" O SER B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.995A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.820A 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 'C' and resid 226 through 232 Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.841A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.715A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 4.223A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.713A pdb=" N LEU C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.594A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 4.198A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.550A pdb=" N ASN D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.819A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.728A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.816A pdb=" N ILE D 428 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.544A pdb=" N ASP D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 removed outlier: 4.807A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 571 through 575 removed outlier: 3.580A pdb=" N VAL D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.784A 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 'E' and resid 226 through 232 Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.752A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 462 through 471 removed outlier: 4.018A pdb=" N LEU E 466 " --> pdb=" O ASN E 462 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 471 " --> pdb=" O LYS E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 511 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 571 through 575 removed outlier: 3.576A pdb=" N VAL E 575 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.228A 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 'F' and resid 226 through 232 removed outlier: 3.765A pdb=" N ASN F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.882A 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 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.919A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 removed outlier: 3.647A pdb=" N SER F 471 " --> pdb=" O LYS F 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 511 Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.991A 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 removed outlier: 4.007A pdb=" N LYS F 661 " --> pdb=" O PRO F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.642A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 250 " --> pdb=" O SER G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.978A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.513A pdb=" N GLY G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 511 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 4.049A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'G' and resid 658 through 662 removed outlier: 3.529A pdb=" N LYS G 661 " --> pdb=" O PRO G 658 " (cutoff:3.500A) 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: 6.689A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 309 removed outlier: 6.689A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.723A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 405 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 483 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN A 481 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 409 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 479 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 411 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 477 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.235A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.859A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.606A pdb=" N THR A 684 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 657 removed outlier: 5.702A pdb=" N ASN A 647 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 730 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 649 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 728 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 651 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 722 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 657 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 720 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 738 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 669 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.505A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.505A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 417 through 422 removed outlier: 6.735A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 405 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 483 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN B 481 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 409 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 479 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 411 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 477 " --> pdb=" O LEU B 411 " (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 removed outlier: 3.529A pdb=" N GLU B 576 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.559A pdb=" N ASN B 559 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 4.098A 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 Processing sheet with id=AB9, first strand: chain 'B' and resid 647 through 656 removed outlier: 6.068A pdb=" N ASN B 647 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 730 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 649 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 728 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 651 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 667 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.866A 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: 5.591A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 417 through 422 removed outlier: 3.875A pdb=" N ALA C 419 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 404 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 485 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 481 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN C 410 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR C 479 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.361A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 576 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 removed outlier: 4.062A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AC8, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.958A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD1, first strand: chain 'D' and resid 299 through 309 removed outlier: 6.774A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 436 " --> pdb=" O ASN D 396 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 299 through 309 removed outlier: 6.774A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 417 through 422 removed outlier: 6.954A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL D 412 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.536A 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: 9.264A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 557 through 558 Processing sheet with id=AD7, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.585A 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 656 removed outlier: 5.761A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 738 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 669 " --> pdb=" O THR D 738 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 708 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY D 672 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 706 " --> pdb=" O GLY D 672 " (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 309 removed outlier: 5.735A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 446 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 417 through 422 removed outlier: 6.795A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS E 404 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY E 484 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 406 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL E 482 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE4, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AE5, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.271A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AE7, first strand: chain 'E' and resid 647 through 656 removed outlier: 6.172A pdb=" N ASN E 647 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE E 730 " --> pdb=" O ASN E 647 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU E 649 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY E 728 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY E 651 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE9, first strand: chain 'F' and resid 299 through 309 removed outlier: 5.498A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 299 through 309 removed outlier: 5.498A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 390 " --> pdb=" O LEU F 448 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 417 through 422 removed outlier: 6.948A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS F 404 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY F 484 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 406 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL F 482 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR F 408 " --> pdb=" O THR F 480 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF4, first strand: chain 'F' and resid 524 through 530 removed outlier: 3.749A pdb=" N LYS F 613 " --> pdb=" O GLU F 576 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU F 576 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 557 through 559 removed outlier: 3.737A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.560A pdb=" N THR F 684 " --> pdb=" O THR F 725 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 647 through 657 removed outlier: 5.720A pdb=" N GLY F 728 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 653 " --> pdb=" O SER F 726 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER F 726 " --> pdb=" O THR F 653 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE F 655 " --> pdb=" O LEU F 724 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU F 724 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 657 " --> pdb=" O ILE F 722 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE F 722 " --> pdb=" O ILE F 657 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 672 " --> pdb=" O PHE F 706 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 234 through 236 Processing sheet with id=AF9, first strand: chain 'G' and resid 299 through 305 removed outlier: 7.166A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 299 through 305 removed outlier: 7.166A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 326 through 329 removed outlier: 3.798A pdb=" N THR G 327 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 365 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER G 363 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 351 through 352 removed outlier: 3.616A pdb=" N LYS G 613 " --> pdb=" O GLU G 576 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 417 through 422 removed outlier: 7.707A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AG6, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AG7, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.125A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 735 " --> pdb=" O THR G 619 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.125A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 735 " --> pdb=" O THR G 619 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG G 667 " --> pdb=" O LEU G 740 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 712 " --> pdb=" O LYS G 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 652 through 656 removed outlier: 3.527A pdb=" N THR G 723 " --> pdb=" O ASN G 686 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.86 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8065 1.34 - 1.46: 4798 1.46 - 1.58: 12286 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 25224 Sorted by residual: bond pdb=" CD2 TRP G 374 " pdb=" CE2 TRP G 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.85e+00 bond pdb=" CD2 TRP E 631 " pdb=" CE2 TRP E 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.82e+00 bond pdb=" CD2 TRP C 244 " pdb=" CE2 TRP C 244 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.76e+00 bond pdb=" CD2 TRP F 631 " pdb=" CE2 TRP F 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.74e+00 bond pdb=" CD2 TRP C 631 " pdb=" CE2 TRP C 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.71e+00 ... (remaining 25219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 33062 1.23 - 2.46: 762 2.46 - 3.68: 170 3.68 - 4.91: 25 4.91 - 6.14: 18 Bond angle restraints: 34037 Sorted by residual: angle pdb=" CD2 TRP B 631 " pdb=" CE3 TRP B 631 " pdb=" CZ3 TRP B 631 " ideal model delta sigma weight residual 118.60 124.03 -5.43 1.30e+00 5.92e-01 1.75e+01 angle pdb=" CD2 TRP C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP G 631 " pdb=" CE3 TRP G 631 " pdb=" CZ3 TRP G 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP E 631 " pdb=" CE3 TRP E 631 " pdb=" CZ3 TRP E 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP D 631 " pdb=" CE3 TRP D 631 " pdb=" CZ3 TRP D 631 " ideal model delta sigma weight residual 118.60 123.96 -5.36 1.30e+00 5.92e-01 1.70e+01 ... (remaining 34032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13837 17.87 - 35.75: 1237 35.75 - 53.62: 198 53.62 - 71.49: 43 71.49 - 89.36: 31 Dihedral angle restraints: 15346 sinusoidal: 6123 harmonic: 9223 Sorted by residual: dihedral pdb=" CA ILE A 459 " pdb=" C ILE A 459 " pdb=" N PRO A 460 " pdb=" CA PRO A 460 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ILE B 459 " pdb=" C ILE B 459 " pdb=" N PRO B 460 " pdb=" CA PRO B 460 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU C 478 " pdb=" CG GLU C 478 " pdb=" CD GLU C 478 " pdb=" OE1 GLU C 478 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2594 0.035 - 0.071: 875 0.071 - 0.106: 329 0.106 - 0.141: 129 0.141 - 0.177: 5 Chirality restraints: 3932 Sorted by residual: 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 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CB ILE F 657 " pdb=" CA ILE F 657 " pdb=" CG1 ILE F 657 " pdb=" CG2 ILE F 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-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 6.73e-01 ... (remaining 3929 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 269 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 459 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO E 460 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 460 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 460 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 290 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 291 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " 0.024 5.00e-02 4.00e+02 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2350 2.75 - 3.29: 23804 3.29 - 3.83: 38544 3.83 - 4.36: 47037 4.36 - 4.90: 83523 Nonbonded interactions: 195258 Sorted by model distance: nonbonded pdb=" OG1 THR G 331 " pdb=" OD2 ASP G 519 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU F 576 " pdb=" OG1 THR F 738 " model vdw 2.226 3.040 nonbonded pdb=" ND2 ASN B 485 " pdb=" O ASN B 500 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR G 220 " pdb=" OD2 ASP G 227 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 616 " pdb=" OE1 GLU A 739 " model vdw 2.255 3.040 ... (remaining 195253 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 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'B' and (resid 216 through 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'C' and (resid 216 through 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'D' and (resid 216 through 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'E' and (resid 216 through 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'F' and (resid 216 through 449 or resid 460 through 742 or resid 901 thro \ ugh 903)) selection = (chain 'G' and (resid 216 through 321 or resid 341 through 342 or resid 356 or r \ esid 388 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 742 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 52.120 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.110 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.051 25224 Z= 0.124 Angle : 0.495 6.141 34037 Z= 0.293 Chirality : 0.044 0.177 3932 Planarity : 0.004 0.059 4426 Dihedral : 14.271 89.362 9308 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3163 helix: -0.87 (0.25), residues: 393 sheet: 1.49 (0.19), residues: 789 loop : -0.80 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 502 HIS 0.000 0.000 HIS G 358 PHE 0.020 0.001 PHE G 579 TYR 0.013 0.001 TYR A 486 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.24830 ( 707) hydrogen bonds : angle 9.01525 ( 1800) covalent geometry : bond 0.00243 (25224) covalent geometry : angle 0.49483 (34037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 2.697 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: C 640 ASP cc_start: 0.8144 (m-30) cc_final: 0.7408 (t0) REVERT: F 402 MET cc_start: 0.7645 (ttm) cc_final: 0.7376 (ttm) REVERT: F 702 ASP cc_start: 0.7473 (t0) cc_final: 0.7104 (m-30) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.3604 time to fit residues: 161.9131 Evaluate side-chains 157 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 129 optimal weight: 50.0000 chunk 250 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 152 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 290 optimal weight: 0.4980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 686 ASN E 647 ASN F 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057007 restraints weight = 81177.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058742 restraints weight = 42089.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059867 restraints weight = 28476.536| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25224 Z= 0.140 Angle : 0.538 7.824 34037 Z= 0.308 Chirality : 0.045 0.183 3932 Planarity : 0.004 0.049 4426 Dihedral : 3.847 20.033 3185 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.70 % Allowed : 6.65 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3163 helix: -0.43 (0.25), residues: 404 sheet: 1.61 (0.18), residues: 790 loop : -0.72 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 374 HIS 0.000 0.000 HIS G 358 PHE 0.011 0.001 PHE B 710 TYR 0.011 0.001 TYR D 703 ARG 0.000 0.000 ARG E 527 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 707) hydrogen bonds : angle 6.19466 ( 1800) covalent geometry : bond 0.00294 (25224) covalent geometry : angle 0.53756 (34037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 175 average time/residue: 0.3285 time to fit residues: 95.8792 Evaluate side-chains 156 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 704 THR Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 360 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 173 optimal weight: 50.0000 chunk 176 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 265 optimal weight: 50.0000 chunk 191 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 243 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 435 ASN B 485 ASN C 391 ASN C 431 ASN F 508 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053906 restraints weight = 82745.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055548 restraints weight = 44616.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056588 restraints weight = 30934.532| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 25224 Z= 0.230 Angle : 0.554 5.406 34037 Z= 0.316 Chirality : 0.045 0.217 3932 Planarity : 0.004 0.045 4426 Dihedral : 4.134 20.355 3185 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.60 % Allowed : 9.88 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3163 helix: -0.56 (0.24), residues: 430 sheet: 1.43 (0.18), residues: 797 loop : -0.79 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 PHE 0.011 0.001 PHE F 710 TYR 0.018 0.001 TYR A 486 ARG 0.000 0.000 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 707) hydrogen bonds : angle 5.67330 ( 1800) covalent geometry : bond 0.00516 (25224) covalent geometry : angle 0.55384 (34037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 ASN cc_start: 0.8743 (p0) cc_final: 0.8495 (t0) REVERT: C 451 MET cc_start: 0.8006 (mtt) cc_final: 0.7129 (tpp) REVERT: E 451 MET cc_start: 0.7848 (tmm) cc_final: 0.7594 (tmm) outliers start: 17 outliers final: 12 residues processed: 155 average time/residue: 0.3408 time to fit residues: 88.5447 Evaluate side-chains 146 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 704 THR Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 587 ILE Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 172 optimal weight: 40.0000 chunk 192 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 155 optimal weight: 0.0570 chunk 207 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 455 ASN E 647 ASN ** E 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055190 restraints weight = 82841.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056871 restraints weight = 43839.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057964 restraints weight = 30156.695| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25224 Z= 0.130 Angle : 0.493 13.402 34037 Z= 0.282 Chirality : 0.044 0.154 3932 Planarity : 0.003 0.046 4426 Dihedral : 3.909 19.655 3185 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.91 % Allowed : 11.08 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3163 helix: -0.31 (0.25), residues: 420 sheet: 1.47 (0.18), residues: 791 loop : -0.67 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.000 HIS G 358 PHE 0.010 0.001 PHE A 670 TYR 0.010 0.001 TYR D 564 ARG 0.000 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 707) hydrogen bonds : angle 5.27850 ( 1800) covalent geometry : bond 0.00276 (25224) covalent geometry : angle 0.49317 (34037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7935 (mtt) cc_final: 0.7045 (tpp) REVERT: C 459 ILE cc_start: 0.8597 (tt) cc_final: 0.8386 (tt) REVERT: E 451 MET cc_start: 0.7889 (tmm) cc_final: 0.7608 (tmm) REVERT: F 402 MET cc_start: 0.8849 (ttm) cc_final: 0.8412 (mtp) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 0.3387 time to fit residues: 92.9109 Evaluate side-chains 148 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 587 ILE Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 251 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 278 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN C 455 ASN E 647 ASN ** E 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.082434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054719 restraints weight = 82874.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056406 restraints weight = 44142.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057473 restraints weight = 30367.415| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25224 Z= 0.146 Angle : 0.496 8.632 34037 Z= 0.284 Chirality : 0.044 0.158 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.899 19.304 3185 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.98 % Allowed : 11.78 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3163 helix: -0.38 (0.24), residues: 430 sheet: 1.32 (0.18), residues: 807 loop : -0.63 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.009 0.001 PHE F 710 TYR 0.010 0.001 TYR A 486 ARG 0.000 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 707) hydrogen bonds : angle 5.15523 ( 1800) covalent geometry : bond 0.00319 (25224) covalent geometry : angle 0.49607 (34037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.8032 (mtt) cc_final: 0.7162 (tpp) REVERT: C 459 ILE cc_start: 0.8520 (tt) cc_final: 0.8314 (tt) REVERT: C 666 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7590 (tttm) REVERT: E 451 MET cc_start: 0.7959 (tmm) cc_final: 0.7676 (tmm) outliers start: 28 outliers final: 15 residues processed: 155 average time/residue: 0.3223 time to fit residues: 85.1223 Evaluate side-chains 139 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 309 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053950 restraints weight = 82582.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055615 restraints weight = 44337.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056660 restraints weight = 30624.303| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25224 Z= 0.163 Angle : 0.508 8.753 34037 Z= 0.288 Chirality : 0.044 0.169 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.943 19.399 3185 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.27 % Allowed : 12.21 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3163 helix: -0.39 (0.24), residues: 430 sheet: 1.29 (0.18), residues: 807 loop : -0.61 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.008 0.001 PHE F 710 TYR 0.012 0.001 TYR A 486 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 707) hydrogen bonds : angle 5.06974 ( 1800) covalent geometry : bond 0.00357 (25224) covalent geometry : angle 0.50842 (34037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7885 (mtt) cc_final: 0.7226 (tpp) REVERT: E 451 MET cc_start: 0.7937 (tmm) cc_final: 0.7684 (tmm) outliers start: 36 outliers final: 24 residues processed: 158 average time/residue: 0.3340 time to fit residues: 90.9589 Evaluate side-chains 147 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 99 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 206 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 254 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 277 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3471 r_free = 0.3471 target = 0.082141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054470 restraints weight = 83158.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056143 restraints weight = 44299.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.057199 restraints weight = 30504.807| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25224 Z= 0.130 Angle : 0.503 8.387 34037 Z= 0.284 Chirality : 0.044 0.189 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.876 19.082 3185 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.06 % Allowed : 12.70 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3163 helix: -0.33 (0.25), residues: 430 sheet: 1.34 (0.18), residues: 807 loop : -0.56 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.000 HIS G 358 PHE 0.007 0.001 PHE F 710 TYR 0.011 0.001 TYR C 387 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 707) hydrogen bonds : angle 4.96897 ( 1800) covalent geometry : bond 0.00279 (25224) covalent geometry : angle 0.50298 (34037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7937 (mtt) cc_final: 0.7232 (tpp) REVERT: E 451 MET cc_start: 0.7955 (tmm) cc_final: 0.7690 (tmm) outliers start: 30 outliers final: 26 residues processed: 156 average time/residue: 0.3002 time to fit residues: 80.7069 Evaluate side-chains 150 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 299 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 219 optimal weight: 50.0000 chunk 66 optimal weight: 9.9990 chunk 284 optimal weight: 40.0000 chunk 190 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3461 r_free = 0.3461 target = 0.081617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053883 restraints weight = 83179.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055548 restraints weight = 44701.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056586 restraints weight = 30808.673| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25224 Z= 0.153 Angle : 0.509 7.513 34037 Z= 0.288 Chirality : 0.044 0.169 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.904 18.991 3185 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.23 % Allowed : 12.66 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3163 helix: -0.33 (0.25), residues: 430 sheet: 1.38 (0.18), residues: 817 loop : -0.57 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.010 0.001 PHE E 706 TYR 0.011 0.001 TYR A 486 ARG 0.000 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 707) hydrogen bonds : angle 4.92508 ( 1800) covalent geometry : bond 0.00336 (25224) covalent geometry : angle 0.50920 (34037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7993 (mtt) cc_final: 0.7300 (tpp) REVERT: E 451 MET cc_start: 0.7962 (tmm) cc_final: 0.7700 (tmm) REVERT: E 594 LEU cc_start: 0.8558 (tp) cc_final: 0.8327 (tp) outliers start: 35 outliers final: 28 residues processed: 148 average time/residue: 0.3121 time to fit residues: 80.1490 Evaluate side-chains 148 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 291 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 193 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 508 GLN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.081557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053802 restraints weight = 83363.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055479 restraints weight = 44808.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056516 restraints weight = 30888.121| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25224 Z= 0.152 Angle : 0.519 12.990 34037 Z= 0.290 Chirality : 0.044 0.160 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.929 19.007 3185 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.13 % Allowed : 12.77 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3163 helix: -0.30 (0.25), residues: 430 sheet: 1.28 (0.18), residues: 833 loop : -0.55 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.007 0.001 PHE A 670 TYR 0.011 0.001 TYR A 486 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 707) hydrogen bonds : angle 4.89978 ( 1800) covalent geometry : bond 0.00333 (25224) covalent geometry : angle 0.51909 (34037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7912 (mtt) cc_final: 0.7278 (tpp) REVERT: D 654 LYS cc_start: 0.5409 (tptt) cc_final: 0.5175 (tptp) REVERT: D 686 ASN cc_start: 0.8621 (m-40) cc_final: 0.8374 (p0) REVERT: E 451 MET cc_start: 0.7948 (tmm) cc_final: 0.7681 (tmm) REVERT: E 594 LEU cc_start: 0.8592 (tp) cc_final: 0.8362 (tp) outliers start: 32 outliers final: 28 residues processed: 147 average time/residue: 0.3088 time to fit residues: 78.7908 Evaluate side-chains 144 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 125 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 274 optimal weight: 0.3980 chunk 295 optimal weight: 1.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 681 ASN ** E 643 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 = 0.3452 r_free = 0.3452 target = 0.081152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053459 restraints weight = 83425.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.055126 restraints weight = 44963.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056164 restraints weight = 31004.734| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25224 Z= 0.170 Angle : 0.533 14.090 34037 Z= 0.295 Chirality : 0.044 0.156 3932 Planarity : 0.003 0.044 4426 Dihedral : 4.002 19.238 3185 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.98 % Allowed : 13.05 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3163 helix: -0.33 (0.25), residues: 432 sheet: 1.25 (0.18), residues: 833 loop : -0.57 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.007 0.001 PHE F 710 TYR 0.012 0.001 TYR A 486 ARG 0.000 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.02772 ( 707) hydrogen bonds : angle 4.90510 ( 1800) covalent geometry : bond 0.00376 (25224) covalent geometry : angle 0.53277 (34037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 2.775 Fit side-chains revert: symmetry clash REVERT: C 451 MET cc_start: 0.7904 (mtt) cc_final: 0.7359 (tpp) REVERT: D 686 ASN cc_start: 0.8585 (m-40) cc_final: 0.8380 (p0) REVERT: E 451 MET cc_start: 0.7947 (tmm) cc_final: 0.7687 (tmm) REVERT: E 594 LEU cc_start: 0.8616 (tp) cc_final: 0.8374 (tp) outliers start: 28 outliers final: 24 residues processed: 141 average time/residue: 0.2998 time to fit residues: 74.0534 Evaluate side-chains 140 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 111 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 43 optimal weight: 50.0000 chunk 253 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 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 = 0.3457 r_free = 0.3457 target = 0.081345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053800 restraints weight = 83240.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055464 restraints weight = 44765.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056500 restraints weight = 30900.135| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25224 Z= 0.147 Angle : 0.520 14.153 34037 Z= 0.289 Chirality : 0.044 0.152 3932 Planarity : 0.003 0.044 4426 Dihedral : 3.960 19.157 3185 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.98 % Allowed : 13.23 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3163 helix: -0.34 (0.25), residues: 432 sheet: 1.25 (0.18), residues: 833 loop : -0.55 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 PHE 0.010 0.001 PHE G 710 TYR 0.011 0.001 TYR A 486 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 707) hydrogen bonds : angle 4.88328 ( 1800) covalent geometry : bond 0.00324 (25224) covalent geometry : angle 0.52006 (34037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6748.19 seconds wall clock time: 118 minutes 49.25 seconds (7129.25 seconds total)