Starting phenix.real_space_refine on Sat Jun 21 07:32:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsm_61777/06_2025/9jsm_61777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsm_61777/06_2025/9jsm_61777.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/9jsm_61777/06_2025/9jsm_61777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsm_61777/06_2025/9jsm_61777.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsm_61777/06_2025/9jsm_61777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsm_61777/06_2025/9jsm_61777.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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 40 5.16 5 C 16020 2.51 5 N 4012 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25209 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3488 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3514 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 433} Chain breaks: 1 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: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3490 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: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3847 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3821 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} 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: 17.24, per 1000 atoms: 0.68 Number of scatterers: 25209 At special positions: 0 Unit cell: (176.88, 176.88, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 40 16.00 O 5116 8.00 N 4012 7.00 C 16020 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: 6.64 Conformation dependent library (CDL) restraints added in 4.0 seconds 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6124 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 66 sheets defined 17.5% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.698A pdb=" N ASN A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.787A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.936A pdb=" N ASP A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.952A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.601A pdb=" N SER A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.619A pdb=" N GLU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.729A 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 233 removed outlier: 3.551A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.652A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 4.155A 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: 3.597A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.596A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 4.007A 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 233 Processing helix chain 'C' and resid 245 through 249 removed outlier: 3.537A pdb=" N ALA C 249 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 424 through 428 removed outlier: 4.134A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.660A pdb=" N VAL C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.553A pdb=" N GLU C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.072A 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 233 Processing helix chain 'D' and resid 245 through 249 removed outlier: 3.500A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.658A pdb=" N ARG D 289 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 471 removed outlier: 4.371A pdb=" N LEU D 466 " --> pdb=" O ASN D 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 505 through 511 removed outlier: 3.792A pdb=" N ILE D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 removed outlier: 3.570A pdb=" N LYS D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 removed outlier: 3.871A pdb=" N VAL D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.602A pdb=" N GLU D 585 " --> pdb=" O ASP D 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 586 " --> pdb=" O ASN D 582 " (cutoff:3.500A) removed outlier: 4.007A 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 233 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.838A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 removed outlier: 3.829A pdb=" N LYS E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 545 through 554 removed outlier: 3.657A pdb=" N LYS E 551 " --> pdb=" O GLY E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 575 removed outlier: 3.840A pdb=" N VAL E 575 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 593 removed outlier: 3.523A pdb=" N ILE E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR E 593 " --> pdb=" O GLU E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.524A pdb=" N ASN F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.733A pdb=" N ALA F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 331 through 336 removed outlier: 3.640A pdb=" N THR F 335 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 502 through 504 No H-bonds generated for 'chain 'F' and resid 502 through 504' Processing helix chain 'F' and resid 505 through 510 Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 571 through 575 removed outlier: 3.810A pdb=" N VAL F 575 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.737A 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 'G' and resid 226 through 233 removed outlier: 3.627A pdb=" N ASN G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 removed outlier: 3.701A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.804A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'G' and resid 462 through 471 removed outlier: 3.548A pdb=" N LEU G 466 " --> pdb=" O ASN G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 512 removed outlier: 3.762A pdb=" N SER G 511 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 512 " --> pdb=" O GLN G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 591 Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'G' and resid 658 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 309 removed outlier: 5.129A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 309 removed outlier: 5.129A pdb=" N VAL A 301 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 395 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET A 303 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 393 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 390 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 3.721A pdb=" N GLN A 481 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN A 410 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 479 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 412 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU A 477 " --> pdb=" O VAL A 412 " (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 513 through 519 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 4.151A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 removed outlier: 3.624A pdb=" N GLU A 576 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.536A pdb=" N TYR A 617 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 684 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 657 removed outlier: 3.865A pdb=" N GLY A 651 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY A 728 " --> pdb=" O GLY A 651 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR A 653 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER A 726 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 655 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A 724 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 657 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 722 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 667 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 712 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 672 " --> pdb=" O PHE A 706 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB4, first strand: chain 'B' and resid 303 through 309 removed outlier: 6.710A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 417 through 422 removed outlier: 3.930A pdb=" N ALA B 419 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 405 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 483 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN B 481 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 409 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR B 479 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU B 411 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 477 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB7, first strand: chain 'B' and resid 524 through 530 removed outlier: 3.618A pdb=" N LYS B 613 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 576 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.321A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 617 through 619 removed outlier: 3.512A pdb=" N THR B 684 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 647 through 657 removed outlier: 5.802A pdb=" N ASN B 647 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE B 730 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 649 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 728 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 651 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 657 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 720 " --> pdb=" O ILE B 657 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 738 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 309 removed outlier: 5.178A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 417 through 422 removed outlier: 6.619A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS C 404 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY C 484 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C 406 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 482 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR C 408 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC6, first strand: chain 'C' and resid 524 through 530 removed outlier: 8.938A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 557 through 559 removed outlier: 4.163A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 617 through 618 Processing sheet with id=AC9, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.830A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 670 " --> pdb=" O TYR C 708 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR C 708 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD2, first strand: chain 'D' and resid 293 through 294 removed outlier: 4.864A pdb=" N ARG D 528 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 613 " --> pdb=" O GLU D 576 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU D 576 " --> pdb=" O LYS D 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 299 through 309 removed outlier: 5.231A pdb=" N VAL D 301 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR D 395 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET D 303 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG D 393 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 305 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 402 through 405 removed outlier: 6.730A pdb=" N ASN D 430 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 417 through 422 removed outlier: 6.545A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR D 408 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 478 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 450 through 452 removed outlier: 7.026A pdb=" N ALA D 456 " --> pdb=" O MET D 451 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD8, first strand: chain 'D' and resid 557 through 558 Processing sheet with id=AD9, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.614A pdb=" N THR D 684 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 647 through 657 removed outlier: 5.839A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 657 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE D 720 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 738 " --> pdb=" O VAL D 669 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE3, first strand: chain 'E' and resid 299 through 309 removed outlier: 5.316A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 299 through 309 removed outlier: 5.316A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 446 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 417 through 422 removed outlier: 4.151A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 478 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 412 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 488 through 489 removed outlier: 3.579A pdb=" N THR E 488 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AE8, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.325A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 617 through 619 removed outlier: 3.601A pdb=" N THR E 725 " --> pdb=" O THR E 684 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR E 684 " --> pdb=" O THR E 725 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 695 " --> pdb=" O VAL E 685 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 687 " --> pdb=" O LYS E 693 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 647 through 656 removed outlier: 5.694A pdb=" N ASN E 647 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE E 730 " --> pdb=" O ASN E 647 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU E 649 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY E 728 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY E 651 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG E 667 " --> pdb=" O LEU E 740 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 670 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR E 708 " --> pdb=" O PHE E 670 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY E 672 " --> pdb=" O PHE E 706 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AF3, first strand: chain 'F' and resid 299 through 303 removed outlier: 3.753A pdb=" N GLU F 436 " --> pdb=" O ASN F 396 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 299 through 303 Processing sheet with id=AF5, first strand: chain 'F' and resid 326 through 329 removed outlier: 3.669A pdb=" N THR F 327 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 329 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER F 363 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 351 through 353 removed outlier: 3.569A pdb=" N PHE F 579 " --> pdb=" O ASN F 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN F 609 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N ILE F 610 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER F 515 " --> pdb=" O ILE F 610 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE F 612 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 517 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 416 through 422 removed outlier: 7.220A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 404 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY F 484 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR F 406 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL F 482 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR F 408 " --> pdb=" O THR F 480 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 557 through 559 Processing sheet with id=AF9, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.906A pdb=" N LEU F 732 " --> pdb=" O ASN F 647 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN F 647 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 619 removed outlier: 8.120A pdb=" N ASP F 733 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LYS F 675 " --> pdb=" O ASP F 733 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU F 735 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR F 673 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE F 737 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER F 671 " --> pdb=" O ILE F 737 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU F 739 " --> pdb=" O VAL F 669 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 669 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN F 741 " --> pdb=" O ARG F 667 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 672 " --> pdb=" O PHE F 706 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 652 through 653 removed outlier: 3.534A pdb=" N ILE F 657 " --> pdb=" O ILE F 720 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 652 through 653 removed outlier: 3.509A pdb=" N GLU F 721 " --> pdb=" O LYS F 688 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AG5, first strand: chain 'G' and resid 293 through 294 removed outlier: 4.720A pdb=" N ARG G 528 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 611 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE G 352 " --> pdb=" O SER G 339 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.948A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 363 through 366 removed outlier: 4.948A pdb=" N GLU G 304 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 328 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY G 302 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 390 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 429 through 432 removed outlier: 6.429A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS G 404 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN G 485 " --> pdb=" O LYS G 404 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 483 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 481 " --> pdb=" O THR G 408 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 557 through 559 removed outlier: 3.569A pdb=" N LEU G 562 " --> pdb=" O ASN G 559 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 617 through 619 Processing sheet with id=AH2, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.536A pdb=" N LEU G 735 " --> pdb=" O SER G 671 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER G 671 " --> pdb=" O LEU G 735 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE G 737 " --> pdb=" O VAL G 669 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 669 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU G 739 " --> pdb=" O ARG G 667 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG G 667 " --> pdb=" O GLU G 739 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 710 " --> pdb=" O TYR G 668 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY G 672 " --> pdb=" O PHE G 706 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 704 " --> pdb=" O SER G 674 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 652 through 657 removed outlier: 3.525A pdb=" N LEU G 724 " --> pdb=" O THR G 653 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 655 " --> pdb=" O ILE G 722 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE G 720 " --> pdb=" O ILE G 657 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 686 " --> pdb=" O THR G 723 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 1824 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: 18.20 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4529 1.27 - 1.41: 5509 1.41 - 1.54: 15398 1.54 - 1.68: 100 1.68 - 1.81: 73 Bond restraints: 25609 Sorted by residual: bond pdb=" C ASN D 485 " pdb=" O ASN D 485 " ideal model delta sigma weight residual 1.233 1.140 0.094 1.31e-02 5.83e+03 5.10e+01 bond pdb=" CD2 TRP D 631 " pdb=" CE2 TRP D 631 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.91e+00 bond pdb=" CD2 TRP B 631 " pdb=" CE2 TRP B 631 " ideal model delta sigma weight residual 1.409 1.447 -0.038 1.70e-02 3.46e+03 4.89e+00 bond pdb=" CD2 TRP A 631 " pdb=" CE2 TRP A 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 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 4.63e+00 ... (remaining 25604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33453 1.40 - 2.80: 912 2.80 - 4.20: 160 4.20 - 5.60: 38 5.60 - 7.01: 4 Bond angle restraints: 34567 Sorted by residual: angle pdb=" CD2 TRP C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 124.08 -5.48 1.30e+00 5.92e-01 1.78e+01 angle pdb=" CD2 TRP D 631 " pdb=" CE3 TRP D 631 " pdb=" CZ3 TRP D 631 " ideal model delta sigma weight residual 118.60 124.00 -5.40 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 G 374 " pdb=" CE3 TRP G 374 " pdb=" CZ3 TRP G 374 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" N VAL B 512 " pdb=" CA VAL B 512 " pdb=" C VAL B 512 " ideal model delta sigma weight residual 113.20 109.22 3.98 9.60e-01 1.09e+00 1.72e+01 ... (remaining 34562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14040 17.95 - 35.91: 1240 35.91 - 53.86: 202 53.86 - 71.82: 40 71.82 - 89.77: 39 Dihedral angle restraints: 15561 sinusoidal: 6201 harmonic: 9360 Sorted by residual: dihedral pdb=" CA ASN D 566 " pdb=" C ASN D 566 " pdb=" N GLY D 567 " pdb=" CA GLY D 567 " ideal model delta harmonic sigma weight residual 180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A 606 " pdb=" C ARG A 606 " pdb=" N GLY A 607 " pdb=" CA GLY A 607 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLN B 453 " pdb=" C GLN B 453 " pdb=" N PHE B 454 " pdb=" CA PHE B 454 " ideal model delta harmonic sigma weight residual -180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 15558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2847 0.043 - 0.087: 814 0.087 - 0.130: 309 0.130 - 0.173: 16 0.173 - 0.216: 3 Chirality restraints: 3989 Sorted by residual: chirality pdb=" CB THR G 406 " pdb=" CA THR G 406 " pdb=" OG1 THR G 406 " pdb=" CG2 THR G 406 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL G 512 " pdb=" CA VAL G 512 " pdb=" CG1 VAL G 512 " pdb=" CG2 VAL G 512 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP G 414 " pdb=" N ASP G 414 " pdb=" C ASP G 414 " pdb=" CB ASP G 414 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 3986 not shown) Planarity restraints: 4502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 536 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO D 537 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 537 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 537 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 698 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO F 699 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 699 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 699 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO D 269 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.034 5.00e-02 4.00e+02 ... (remaining 4499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2460 2.74 - 3.28: 24904 3.28 - 3.82: 39509 3.82 - 4.36: 47494 4.36 - 4.90: 82866 Nonbonded interactions: 197233 Sorted by model distance: nonbonded pdb=" OD1 ASN A 430 " pdb=" OG SER B 483 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR F 364 " pdb=" O ILE F 475 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU E 721 " pdb=" OG1 THR E 723 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 265 " pdb=" OD2 ASP B 272 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 309 " pdb=" ND2 ASN C 462 " model vdw 2.244 3.120 ... (remaining 197228 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 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'B' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'C' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'D' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'E' and (resid 216 through 295 or resid 297 through 308 or resid 310 thro \ ugh 386 or resid 388 through 449 or resid 459 through 741 or resid 801 through 8 \ 03)) selection = (chain 'F' and (resid 216 through 295 or resid 297 through 308 or resid 326 or r \ esid 341 through 342 or resid 388 through 449 or resid 459 through 614 or (resid \ 615 and (name N or name CA or name C or name O or name CB or name CG )) or resi \ d 616 through 741 or resid 801 through 803)) selection = (chain 'G' and (resid 216 through 295 or resid 297 through 307 or resid 340 or r \ esid 354 through 355 or resid 365 or resid 380 through 381 or resid 390 through \ 614 or (resid 615 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 616 through 741 or resid 801 through 803)) } 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: 2.930 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: 0.040 Extract box with map and model: 1.870 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 73.710 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.140 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:3.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 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 : 0.004 0.094 25609 Z= 0.185 Angle : 0.576 7.006 34567 Z= 0.335 Chirality : 0.045 0.216 3989 Planarity : 0.004 0.103 4502 Dihedral : 14.621 89.771 9437 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3216 helix: -1.34 (0.24), residues: 410 sheet: 0.45 (0.19), residues: 811 loop : -0.94 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 244 HIS 0.001 0.001 HIS F 358 PHE 0.021 0.001 PHE D 454 TYR 0.019 0.001 TYR G 356 ARG 0.000 0.000 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.28450 ( 709) hydrogen bonds : angle 10.05731 ( 1824) covalent geometry : bond 0.00399 (25609) covalent geometry : angle 0.57640 (34567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 2.940 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: symmetry clash REVERT: D 552 LYS cc_start: 0.7208 (mtmm) cc_final: 0.6743 (mtmm) outliers start: 5 outliers final: 2 residues processed: 307 average time/residue: 0.3454 time to fit residues: 172.4902 Evaluate side-chains 172 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain F residue 528 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 40.0000 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 253 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 189 optimal weight: 50.0000 chunk 294 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN C 523 GLN D 601 ASN D 692 GLN E 453 GLN F 435 ASN F 492 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.068554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051896 restraints weight = 129972.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053274 restraints weight = 72543.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054187 restraints weight = 49157.732| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25609 Z= 0.155 Angle : 0.581 7.762 34567 Z= 0.328 Chirality : 0.045 0.262 3989 Planarity : 0.004 0.068 4502 Dihedral : 4.569 59.249 3242 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 6.93 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3216 helix: -0.61 (0.24), residues: 424 sheet: 0.59 (0.18), residues: 825 loop : -0.79 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 502 HIS 0.000 0.000 HIS G 358 PHE 0.018 0.001 PHE B 670 TYR 0.017 0.001 TYR G 463 ARG 0.000 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 709) hydrogen bonds : angle 6.44883 ( 1824) covalent geometry : bond 0.00328 (25609) covalent geometry : angle 0.58130 (34567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LEU cc_start: 0.9335 (mm) cc_final: 0.9132 (mm) REVERT: A 691 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 519 ASP cc_start: 0.8519 (t0) cc_final: 0.8317 (t0) REVERT: C 562 LEU cc_start: 0.8705 (tp) cc_final: 0.8404 (tt) REVERT: D 517 ILE cc_start: 0.9086 (mt) cc_final: 0.8810 (tt) REVERT: E 489 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7935 (tmtt) REVERT: E 548 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8765 (pt0) outliers start: 35 outliers final: 20 residues processed: 204 average time/residue: 0.4537 time to fit residues: 153.3850 Evaluate side-chains 172 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 601 ASN Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 548 GLU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 294 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 chunk 275 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN E 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050644 restraints weight = 130607.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052019 restraints weight = 72630.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052928 restraints weight = 48893.463| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25609 Z= 0.162 Angle : 0.560 12.215 34567 Z= 0.312 Chirality : 0.045 0.284 3989 Planarity : 0.004 0.055 4502 Dihedral : 4.487 54.571 3242 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.18 % Allowed : 9.91 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3216 helix: -0.40 (0.25), residues: 424 sheet: 0.62 (0.18), residues: 844 loop : -0.75 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 502 HIS 0.002 0.001 HIS G 358 PHE 0.010 0.001 PHE G 565 TYR 0.011 0.001 TYR G 356 ARG 0.000 0.000 ARG F 667 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 709) hydrogen bonds : angle 5.75214 ( 1824) covalent geometry : bond 0.00343 (25609) covalent geometry : angle 0.56021 (34567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 411 LEU cc_start: 0.9346 (mm) cc_final: 0.9103 (mm) REVERT: C 519 ASP cc_start: 0.8626 (t0) cc_final: 0.8390 (t0) REVERT: C 591 LEU cc_start: 0.8922 (pp) cc_final: 0.8387 (mt) REVERT: C 594 LEU cc_start: 0.8595 (tp) cc_final: 0.8367 (tp) REVERT: D 517 ILE cc_start: 0.9169 (mt) cc_final: 0.8823 (tt) REVERT: E 436 GLU cc_start: 0.8180 (tp30) cc_final: 0.7796 (tp30) REVERT: E 489 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7945 (tmtt) REVERT: E 519 ASP cc_start: 0.8840 (t0) cc_final: 0.8585 (t0) outliers start: 34 outliers final: 22 residues processed: 183 average time/residue: 0.3529 time to fit residues: 110.7254 Evaluate side-chains 169 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 267 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 319 optimal weight: 30.0000 chunk 233 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 253 optimal weight: 0.3980 chunk 312 optimal weight: 8.9990 chunk 229 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 435 ASN ** G 465 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 = 0.3558 r_free = 0.3558 target = 0.067976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051560 restraints weight = 131119.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052948 restraints weight = 72643.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053858 restraints weight = 48851.709| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25609 Z= 0.115 Angle : 0.514 9.377 34567 Z= 0.288 Chirality : 0.044 0.167 3989 Planarity : 0.003 0.052 4502 Dihedral : 4.158 55.627 3242 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.87 % Allowed : 11.30 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3216 helix: -0.17 (0.25), residues: 427 sheet: 0.68 (0.18), residues: 864 loop : -0.60 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE F 670 TYR 0.009 0.001 TYR C 708 ARG 0.000 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 709) hydrogen bonds : angle 5.29893 ( 1824) covalent geometry : bond 0.00238 (25609) covalent geometry : angle 0.51398 (34567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LEU cc_start: 0.9355 (mm) cc_final: 0.9141 (mm) REVERT: A 691 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 670 PHE cc_start: 0.8374 (t80) cc_final: 0.8083 (t80) REVERT: C 519 ASP cc_start: 0.8552 (t0) cc_final: 0.8072 (t0) REVERT: C 591 LEU cc_start: 0.8934 (pp) cc_final: 0.8401 (mt) REVERT: C 594 LEU cc_start: 0.8547 (tp) cc_final: 0.8328 (tp) REVERT: C 705 LYS cc_start: 0.8342 (tptp) cc_final: 0.8048 (tptp) REVERT: D 451 MET cc_start: 0.8095 (ppp) cc_final: 0.7860 (ppp) REVERT: D 517 ILE cc_start: 0.9176 (mt) cc_final: 0.8826 (tt) REVERT: E 519 ASP cc_start: 0.8895 (t0) cc_final: 0.8633 (t0) REVERT: F 340 ILE cc_start: 0.9192 (mp) cc_final: 0.8894 (mm) REVERT: F 352 ILE cc_start: 0.9054 (mm) cc_final: 0.8642 (mm) REVERT: F 709 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8180 (mp0) REVERT: G 649 LEU cc_start: 0.8343 (mm) cc_final: 0.7945 (tp) REVERT: G 659 MET cc_start: 0.7985 (tpt) cc_final: 0.7731 (tpt) outliers start: 25 outliers final: 12 residues processed: 186 average time/residue: 0.3225 time to fit residues: 102.0689 Evaluate side-chains 160 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 277 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 40.0000 chunk 262 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 187 optimal weight: 0.4980 chunk 108 optimal weight: 0.4980 chunk 215 optimal weight: 50.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 465 GLN G 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.067678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051417 restraints weight = 131652.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052781 restraints weight = 73573.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053684 restraints weight = 49577.304| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25609 Z= 0.119 Angle : 0.517 8.625 34567 Z= 0.289 Chirality : 0.044 0.177 3989 Planarity : 0.003 0.050 4502 Dihedral : 3.950 38.317 3238 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.90 % Allowed : 12.30 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3216 helix: -0.12 (0.25), residues: 433 sheet: 0.76 (0.18), residues: 819 loop : -0.58 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE G 565 TYR 0.010 0.001 TYR C 708 ARG 0.000 0.000 ARG D 457 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 709) hydrogen bonds : angle 5.14259 ( 1824) covalent geometry : bond 0.00247 (25609) covalent geometry : angle 0.51656 (34567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8603 (tp) REVERT: A 411 LEU cc_start: 0.9389 (mm) cc_final: 0.9182 (mm) REVERT: A 691 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 721 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: B 451 MET cc_start: 0.6879 (tpp) cc_final: 0.6636 (mmm) REVERT: B 519 ASP cc_start: 0.7857 (t0) cc_final: 0.7629 (t0) REVERT: B 594 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8557 (tt) REVERT: B 652 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8587 (tp30) REVERT: C 451 MET cc_start: 0.7940 (ttt) cc_final: 0.7629 (ttp) REVERT: C 519 ASP cc_start: 0.8594 (t0) cc_final: 0.8372 (t0) REVERT: C 591 LEU cc_start: 0.8948 (pp) cc_final: 0.8411 (mt) REVERT: C 594 LEU cc_start: 0.8521 (tp) cc_final: 0.8290 (tp) REVERT: C 705 LYS cc_start: 0.8346 (tptp) cc_final: 0.8067 (tptp) REVERT: D 517 ILE cc_start: 0.9175 (mt) cc_final: 0.8832 (tt) REVERT: E 519 ASP cc_start: 0.8847 (t0) cc_final: 0.8621 (t0) REVERT: F 340 ILE cc_start: 0.9165 (mp) cc_final: 0.8753 (mm) REVERT: F 352 ILE cc_start: 0.9039 (mm) cc_final: 0.8620 (mm) REVERT: F 709 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7932 (mp0) REVERT: G 649 LEU cc_start: 0.8320 (mm) cc_final: 0.7931 (tp) outliers start: 26 outliers final: 16 residues processed: 180 average time/residue: 0.3208 time to fit residues: 98.3911 Evaluate side-chains 169 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 167 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 175 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 37 optimal weight: 0.0870 chunk 283 optimal weight: 20.0000 chunk 289 optimal weight: 0.9990 chunk 88 optimal weight: 50.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN D 264 ASN D 686 ASN E 504 ASN F 435 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.066580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050363 restraints weight = 132034.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051693 restraints weight = 73744.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052587 restraints weight = 49715.019| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.143 Angle : 0.532 11.699 34567 Z= 0.297 Chirality : 0.044 0.228 3989 Planarity : 0.003 0.049 4502 Dihedral : 4.028 37.759 3238 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.18 % Allowed : 12.89 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3216 helix: -0.07 (0.25), residues: 433 sheet: 0.67 (0.18), residues: 845 loop : -0.56 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 PHE 0.027 0.001 PHE B 670 TYR 0.011 0.001 TYR E 708 ARG 0.000 0.000 ARG G 393 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 709) hydrogen bonds : angle 5.07963 ( 1824) covalent geometry : bond 0.00303 (25609) covalent geometry : angle 0.53244 (34567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (tp) REVERT: A 721 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: B 594 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 652 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8604 (tp30) REVERT: C 451 MET cc_start: 0.7987 (ttt) cc_final: 0.7680 (ttp) REVERT: C 519 ASP cc_start: 0.8670 (t0) cc_final: 0.8454 (t0) REVERT: C 591 LEU cc_start: 0.8990 (pp) cc_final: 0.8451 (mt) REVERT: C 594 LEU cc_start: 0.8509 (tp) cc_final: 0.8247 (tp) REVERT: C 661 LYS cc_start: 0.8672 (tptp) cc_final: 0.8120 (tttt) REVERT: C 705 LYS cc_start: 0.8270 (tptp) cc_final: 0.8039 (tptp) REVERT: D 517 ILE cc_start: 0.9205 (mt) cc_final: 0.8874 (tt) REVERT: G 498 GLU cc_start: 0.8377 (tp30) cc_final: 0.8027 (tp30) REVERT: G 649 LEU cc_start: 0.8268 (mm) cc_final: 0.7879 (tp) REVERT: G 659 MET cc_start: 0.8066 (tpt) cc_final: 0.7861 (tpt) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 0.3132 time to fit residues: 97.7098 Evaluate side-chains 174 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 75 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 263 optimal weight: 0.0270 chunk 65 optimal weight: 0.0270 chunk 68 optimal weight: 20.0000 chunk 118 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 overall best weight: 4.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 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 = 0.3529 r_free = 0.3529 target = 0.066509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050330 restraints weight = 132739.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051676 restraints weight = 74099.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052568 restraints weight = 49810.957| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.134 Angle : 0.525 10.939 34567 Z= 0.293 Chirality : 0.044 0.193 3989 Planarity : 0.003 0.049 4502 Dihedral : 4.023 37.163 3238 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.52 % Allowed : 12.96 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3216 helix: 0.01 (0.25), residues: 434 sheet: 0.65 (0.18), residues: 858 loop : -0.52 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 PHE 0.008 0.001 PHE G 565 TYR 0.009 0.001 TYR E 708 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 709) hydrogen bonds : angle 5.00140 ( 1824) covalent geometry : bond 0.00282 (25609) covalent geometry : angle 0.52466 (34567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 414 ASP cc_start: 0.8315 (t0) cc_final: 0.7601 (p0) REVERT: A 691 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 721 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: B 451 MET cc_start: 0.7413 (mmm) cc_final: 0.7159 (mmm) REVERT: B 454 PHE cc_start: 0.6634 (m-80) cc_final: 0.6420 (m-80) REVERT: B 594 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 652 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8666 (tp30) REVERT: B 670 PHE cc_start: 0.8476 (t80) cc_final: 0.8254 (t80) REVERT: C 451 MET cc_start: 0.7990 (ttt) cc_final: 0.7689 (ttp) REVERT: C 591 LEU cc_start: 0.8995 (pp) cc_final: 0.8469 (mt) REVERT: C 594 LEU cc_start: 0.8515 (tp) cc_final: 0.8276 (tp) REVERT: C 661 LYS cc_start: 0.8713 (tptp) cc_final: 0.8132 (tttt) REVERT: D 517 ILE cc_start: 0.9203 (mt) cc_final: 0.8881 (tt) REVERT: E 440 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8450 (tttm) REVERT: F 352 ILE cc_start: 0.8906 (mm) cc_final: 0.8460 (mm) REVERT: F 659 MET cc_start: 0.8232 (tpt) cc_final: 0.7564 (tpp) REVERT: F 709 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8308 (mp0) REVERT: G 498 GLU cc_start: 0.8356 (tp30) cc_final: 0.7994 (tp30) REVERT: G 649 LEU cc_start: 0.8304 (mm) cc_final: 0.7919 (tp) outliers start: 44 outliers final: 30 residues processed: 190 average time/residue: 0.3063 time to fit residues: 99.9758 Evaluate side-chains 181 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 254 optimal weight: 10.0000 chunk 151 optimal weight: 0.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 4.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.066273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050153 restraints weight = 132833.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051491 restraints weight = 74357.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052366 restraints weight = 50312.802| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.136 Angle : 0.533 10.920 34567 Z= 0.297 Chirality : 0.044 0.198 3989 Planarity : 0.003 0.052 4502 Dihedral : 4.036 36.698 3238 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.35 % Allowed : 13.24 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.15), residues: 3216 helix: 0.08 (0.25), residues: 434 sheet: 0.66 (0.18), residues: 886 loop : -0.52 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 631 HIS 0.001 0.000 HIS G 358 PHE 0.014 0.001 PHE F 670 TYR 0.009 0.001 TYR E 708 ARG 0.000 0.000 ARG E 289 Details of bonding type rmsd hydrogen bonds : bond 0.02690 ( 709) hydrogen bonds : angle 5.00920 ( 1824) covalent geometry : bond 0.00287 (25609) covalent geometry : angle 0.53277 (34567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8550 (tp) REVERT: A 414 ASP cc_start: 0.8237 (t0) cc_final: 0.7538 (p0) REVERT: A 519 ASP cc_start: 0.9063 (t0) cc_final: 0.8806 (t0) REVERT: A 691 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 451 MET cc_start: 0.7598 (mmm) cc_final: 0.7095 (mmm) REVERT: B 454 PHE cc_start: 0.6826 (m-80) cc_final: 0.6615 (m-80) REVERT: B 594 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8481 (tt) REVERT: B 652 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8690 (tp30) REVERT: C 451 MET cc_start: 0.8001 (ttt) cc_final: 0.7706 (ttp) REVERT: C 519 ASP cc_start: 0.8517 (t0) cc_final: 0.8308 (t0) REVERT: C 591 LEU cc_start: 0.9029 (pp) cc_final: 0.8529 (mt) REVERT: C 594 LEU cc_start: 0.8534 (tp) cc_final: 0.8292 (tp) REVERT: C 661 LYS cc_start: 0.8675 (tptp) cc_final: 0.7960 (mptt) REVERT: D 517 ILE cc_start: 0.9162 (mt) cc_final: 0.8879 (tt) REVERT: E 440 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8432 (tttm) REVERT: F 352 ILE cc_start: 0.8911 (mm) cc_final: 0.8427 (mm) REVERT: F 709 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8274 (mp0) REVERT: G 498 GLU cc_start: 0.8453 (tp30) cc_final: 0.8075 (tp30) outliers start: 39 outliers final: 28 residues processed: 184 average time/residue: 0.3361 time to fit residues: 108.9992 Evaluate side-chains 176 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 290 optimal weight: 20.0000 chunk 18 optimal weight: 50.0000 chunk 299 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN G 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.064549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048420 restraints weight = 134483.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049718 restraints weight = 75576.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050592 restraints weight = 51402.318| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25609 Z= 0.209 Angle : 0.597 10.123 34567 Z= 0.329 Chirality : 0.044 0.183 3989 Planarity : 0.003 0.054 4502 Dihedral : 4.477 36.728 3238 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 13.62 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3216 helix: -0.02 (0.25), residues: 430 sheet: 0.61 (0.18), residues: 837 loop : -0.64 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 PHE 0.030 0.002 PHE B 670 TYR 0.017 0.001 TYR E 708 ARG 0.000 0.000 ARG B 667 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 709) hydrogen bonds : angle 5.24454 ( 1824) covalent geometry : bond 0.00449 (25609) covalent geometry : angle 0.59728 (34567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 414 ASP cc_start: 0.8195 (t0) cc_final: 0.7603 (p0) REVERT: A 519 ASP cc_start: 0.9143 (t0) cc_final: 0.8891 (t0) REVERT: B 451 MET cc_start: 0.7829 (mmm) cc_final: 0.7394 (mmm) REVERT: B 454 PHE cc_start: 0.6944 (m-80) cc_final: 0.6722 (m-80) REVERT: B 594 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8519 (tt) REVERT: B 652 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8677 (mm-30) REVERT: C 594 LEU cc_start: 0.8549 (tp) cc_final: 0.8289 (tp) REVERT: C 661 LYS cc_start: 0.8716 (tptp) cc_final: 0.7991 (mptt) REVERT: D 517 ILE cc_start: 0.9176 (mt) cc_final: 0.8924 (tt) REVERT: D 740 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6586 (mp) REVERT: E 262 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: F 659 MET cc_start: 0.8370 (tpt) cc_final: 0.7783 (tpp) REVERT: G 402 MET cc_start: 0.8921 (tpp) cc_final: 0.8592 (ttt) REVERT: G 498 GLU cc_start: 0.8558 (tp30) cc_final: 0.8314 (tp30) outliers start: 36 outliers final: 28 residues processed: 174 average time/residue: 0.3416 time to fit residues: 102.9162 Evaluate side-chains 170 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 570 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 431 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 192 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 93 optimal weight: 0.1980 chunk 196 optimal weight: 6.9990 chunk 210 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 233 optimal weight: 30.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.066297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050269 restraints weight = 132918.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051607 restraints weight = 73905.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052498 restraints weight = 49902.253| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25609 Z= 0.117 Angle : 0.547 11.389 34567 Z= 0.300 Chirality : 0.044 0.204 3989 Planarity : 0.003 0.054 4502 Dihedral : 4.051 36.899 3238 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.90 % Allowed : 14.17 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3216 helix: 0.27 (0.26), residues: 425 sheet: 0.67 (0.18), residues: 904 loop : -0.51 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 244 HIS 0.001 0.000 HIS F 358 PHE 0.013 0.001 PHE F 670 TYR 0.009 0.001 TYR G 564 ARG 0.000 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 709) hydrogen bonds : angle 4.98359 ( 1824) covalent geometry : bond 0.00244 (25609) covalent geometry : angle 0.54736 (34567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 ASP cc_start: 0.8216 (t0) cc_final: 0.7632 (p0) REVERT: A 691 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 451 MET cc_start: 0.7711 (mmm) cc_final: 0.7393 (mmm) REVERT: B 594 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 652 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8703 (tp30) REVERT: B 670 PHE cc_start: 0.8601 (t80) cc_final: 0.8394 (t80) REVERT: C 594 LEU cc_start: 0.8531 (tp) cc_final: 0.8296 (tp) REVERT: C 661 LYS cc_start: 0.8652 (tptp) cc_final: 0.7967 (mptt) REVERT: D 517 ILE cc_start: 0.9163 (mt) cc_final: 0.8901 (tt) REVERT: D 740 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6721 (mp) REVERT: E 440 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8372 (tttm) REVERT: F 352 ILE cc_start: 0.8814 (mm) cc_final: 0.8338 (mm) REVERT: F 608 MET cc_start: 0.8618 (mtt) cc_final: 0.8390 (mtt) REVERT: F 659 MET cc_start: 0.8349 (tpt) cc_final: 0.7700 (tpp) REVERT: F 709 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8023 (mp0) outliers start: 26 outliers final: 21 residues processed: 171 average time/residue: 0.3771 time to fit residues: 110.1783 Evaluate side-chains 168 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 698 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 464 ASP Chi-restraints excluded: chain G residue 476 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 205 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 GLN ** B 465 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 = 0.3497 r_free = 0.3497 target = 0.065068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049136 restraints weight = 133944.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050456 restraints weight = 75117.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051277 restraints weight = 50862.691| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25609 Z= 0.161 Angle : 0.565 11.503 34567 Z= 0.310 Chirality : 0.044 0.155 3989 Planarity : 0.003 0.054 4502 Dihedral : 4.114 23.180 3236 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.94 % Allowed : 14.31 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3216 helix: 0.18 (0.25), residues: 431 sheet: 0.63 (0.18), residues: 880 loop : -0.55 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 244 HIS 0.001 0.000 HIS G 358 PHE 0.009 0.001 PHE A 621 TYR 0.012 0.001 TYR E 708 ARG 0.000 0.000 ARG G 667 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 709) hydrogen bonds : angle 5.03155 ( 1824) covalent geometry : bond 0.00343 (25609) covalent geometry : angle 0.56515 (34567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7023.95 seconds wall clock time: 125 minutes 41.55 seconds (7541.55 seconds total)