Starting phenix.real_space_refine on Fri Sep 19 07:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsn_61778/09_2025/9jsn_61778.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 41 5.16 5 C 15792 2.51 5 N 3946 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24834 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3486 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3494 Classifications: {'peptide': 451} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3857 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.26, per 1000 atoms: 0.25 Number of scatterers: 24834 At special positions: 0 Unit cell: (176.88, 176, 95.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 41 16.00 O 5034 8.00 N 3946 7.00 C 15792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 63 sheets defined 18.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.526A pdb=" N ALA A 249 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.917A pdb=" N ASP A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.109A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.760A pdb=" N LYS A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.847A pdb=" N ASN A 504 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.734A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.869A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.862A pdb=" N GLU B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.906A pdb=" N ASP B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 4.157A pdb=" N ILE B 428 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.807A pdb=" N LYS B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 504 removed outlier: 3.825A pdb=" N ASN B 504 " --> pdb=" O SER B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 571 through 575 removed outlier: 3.995A pdb=" N VAL B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.820A pdb=" N LYS B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.841A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.715A pdb=" N ASP C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 4.223A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.713A pdb=" N LEU C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 571 through 575 removed outlier: 3.594A pdb=" N VAL C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 4.198A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR C 593 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.550A pdb=" N ASN D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.819A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.728A pdb=" N ASP D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.816A pdb=" N ILE D 428 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.544A pdb=" N ASP D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 removed outlier: 4.807A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 571 through 575 removed outlier: 3.580A pdb=" N VAL D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.784A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.752A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 462 through 471 removed outlier: 4.018A pdb=" N LEU E 466 " --> pdb=" O ASN E 462 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 471 " --> pdb=" O LYS E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 511 Processing helix chain 'E' and resid 545 through 555 Processing helix chain 'E' and resid 571 through 575 removed outlier: 3.576A pdb=" N VAL E 575 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.228A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.765A pdb=" N ASN F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.882A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.919A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 removed outlier: 3.647A pdb=" N SER F 471 " --> pdb=" O LYS F 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 472 " --> pdb=" O LYS F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 511 Processing helix chain 'F' and resid 545 through 555 Processing helix chain 'F' and resid 580 through 592 removed outlier: 3.991A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 658 through 662 removed outlier: 4.007A pdb=" N LYS F 661 " --> pdb=" O PRO F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.642A pdb=" N ALA G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 250 " --> pdb=" O SER G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 290 removed outlier: 3.978A pdb=" N ASP G 290 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 removed outlier: 3.513A pdb=" N GLY G 472 " --> pdb=" O LYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 511 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 580 through 592 removed outlier: 4.049A pdb=" N LYS G 592 " --> pdb=" O LYS G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'G' and resid 658 through 662 removed outlier: 3.529A pdb=" N LYS G 661 " --> pdb=" O PRO G 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 309 removed outlier: 6.689A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 309 removed outlier: 6.689A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 422 removed outlier: 6.723A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 405 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 483 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN A 481 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 409 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 479 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 411 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 477 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.235A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.859A pdb=" N LEU A 562 " --> pdb=" O ASN A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 removed outlier: 3.606A pdb=" N THR A 684 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 657 removed outlier: 5.702A pdb=" N ASN A 647 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A 730 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 649 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 728 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 651 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 722 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 657 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 720 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 732 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 675 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASN A 734 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 673 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 738 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 669 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.505A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 309 removed outlier: 5.505A pdb=" N VAL B 301 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR B 395 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET B 303 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 393 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 305 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 417 through 422 removed outlier: 6.735A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 405 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 483 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN B 481 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 409 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 479 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 411 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 477 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 530 removed outlier: 3.529A pdb=" N GLU B 576 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.559A pdb=" N ASN B 559 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AB9, first strand: chain 'B' and resid 647 through 656 removed outlier: 6.068A pdb=" N ASN B 647 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 730 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 649 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 728 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 651 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 722 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU B 732 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS B 675 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN B 734 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 673 " --> pdb=" O ASN B 734 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 667 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 672 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 309 removed outlier: 5.591A pdb=" N VAL C 301 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 395 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N MET C 303 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG C 393 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 305 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 417 through 422 removed outlier: 3.875A pdb=" N ALA C 419 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 404 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 485 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 481 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN C 410 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR C 479 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 524 through 530 removed outlier: 9.361A pdb=" N ILE C 610 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 515 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE C 612 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 517 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 576 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 removed outlier: 4.062A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 617 through 619 Processing sheet with id=AC8, first strand: chain 'C' and resid 647 through 656 removed outlier: 5.958A pdb=" N ASN C 647 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 730 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 649 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY C 728 " --> pdb=" O LEU C 649 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY C 651 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 722 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 732 " --> pdb=" O LYS C 675 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 675 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN C 734 " --> pdb=" O TYR C 673 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 673 " --> pdb=" O ASN C 734 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 672 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AD1, first strand: chain 'D' and resid 299 through 309 removed outlier: 6.774A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 436 " --> pdb=" O ASN D 396 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 299 through 309 removed outlier: 6.774A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 417 through 422 removed outlier: 6.954A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS D 404 " --> pdb=" O ASN D 485 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN D 485 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 481 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN D 410 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 479 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL D 412 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU D 477 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD5, first strand: chain 'D' and resid 524 through 530 removed outlier: 9.264A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 557 through 558 Processing sheet with id=AD7, first strand: chain 'D' and resid 617 through 619 removed outlier: 3.585A pdb=" N THR D 684 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 647 through 656 removed outlier: 5.761A pdb=" N ASN D 647 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 730 " --> pdb=" O ASN D 647 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 649 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY D 728 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY D 651 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 722 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU D 732 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS D 675 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN D 734 " --> pdb=" O TYR D 673 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 673 " --> pdb=" O ASN D 734 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 738 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 669 " --> pdb=" O THR D 738 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 708 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY D 672 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 706 " --> pdb=" O GLY D 672 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AE1, first strand: chain 'E' and resid 299 through 309 removed outlier: 5.735A pdb=" N VAL E 301 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR E 395 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N MET E 303 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG E 393 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 305 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 446 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 417 through 422 removed outlier: 6.795A pdb=" N LEU E 411 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR E 420 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR E 409 " --> pdb=" O THR E 420 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS E 422 " --> pdb=" O PRO E 407 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS E 404 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY E 484 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 406 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL E 482 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AE4, first strand: chain 'E' and resid 524 through 530 Processing sheet with id=AE5, first strand: chain 'E' and resid 557 through 559 removed outlier: 4.271A pdb=" N LEU E 562 " --> pdb=" O ASN E 559 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 617 through 619 Processing sheet with id=AE7, first strand: chain 'E' and resid 647 through 656 removed outlier: 6.172A pdb=" N ASN E 647 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE E 730 " --> pdb=" O ASN E 647 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU E 649 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY E 728 " --> pdb=" O LEU E 649 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY E 651 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 722 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU E 732 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS E 675 " --> pdb=" O LEU E 732 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN E 734 " --> pdb=" O TYR E 673 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR E 673 " --> pdb=" O ASN E 734 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE9, first strand: chain 'F' and resid 299 through 309 removed outlier: 5.498A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 299 through 309 removed outlier: 5.498A pdb=" N VAL F 301 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR F 395 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N MET F 303 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 393 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 390 " --> pdb=" O LEU F 448 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 417 through 422 removed outlier: 6.948A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS F 404 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY F 484 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 406 " --> pdb=" O VAL F 482 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL F 482 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR F 408 " --> pdb=" O THR F 480 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 488 through 489 Processing sheet with id=AF4, first strand: chain 'F' and resid 524 through 530 removed outlier: 3.749A pdb=" N LYS F 613 " --> pdb=" O GLU F 576 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU F 576 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 557 through 559 removed outlier: 3.737A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 617 through 619 removed outlier: 3.560A pdb=" N THR F 684 " --> pdb=" O THR F 725 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 647 through 657 removed outlier: 5.720A pdb=" N GLY F 728 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 653 " --> pdb=" O SER F 726 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER F 726 " --> pdb=" O THR F 653 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE F 655 " --> pdb=" O LEU F 724 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU F 724 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 657 " --> pdb=" O ILE F 722 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE F 722 " --> pdb=" O ILE F 657 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU F 732 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS F 675 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN F 734 " --> pdb=" O TYR F 673 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR F 673 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 672 " --> pdb=" O PHE F 706 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 234 through 236 Processing sheet with id=AF9, first strand: chain 'G' and resid 299 through 305 removed outlier: 7.166A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 299 through 305 removed outlier: 7.166A pdb=" N ASN G 391 " --> pdb=" O GLU G 304 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 326 through 329 removed outlier: 3.798A pdb=" N THR G 327 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 365 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER G 363 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 351 through 352 removed outlier: 3.616A pdb=" N LYS G 613 " --> pdb=" O GLU G 576 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 417 through 422 removed outlier: 7.707A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AG6, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AG7, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.125A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 735 " --> pdb=" O THR G 619 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 617 through 619 removed outlier: 4.125A pdb=" N TYR G 617 " --> pdb=" O ILE G 737 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 735 " --> pdb=" O THR G 619 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU G 732 " --> pdb=" O LYS G 675 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS G 675 " --> pdb=" O LEU G 732 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN G 734 " --> pdb=" O TYR G 673 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR G 673 " --> pdb=" O ASN G 734 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG G 667 " --> pdb=" O LEU G 740 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 712 " --> pdb=" O LYS G 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 652 through 656 removed outlier: 3.527A pdb=" N THR G 723 " --> pdb=" O ASN G 686 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8065 1.34 - 1.46: 4798 1.46 - 1.58: 12286 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 25224 Sorted by residual: bond pdb=" CD2 TRP G 374 " pdb=" CE2 TRP G 374 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.85e+00 bond pdb=" CD2 TRP E 631 " pdb=" CE2 TRP E 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.82e+00 bond pdb=" CD2 TRP C 244 " pdb=" CE2 TRP C 244 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.76e+00 bond pdb=" CD2 TRP F 631 " pdb=" CE2 TRP F 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.74e+00 bond pdb=" CD2 TRP C 631 " pdb=" CE2 TRP C 631 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.71e+00 ... (remaining 25219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 33062 1.23 - 2.46: 762 2.46 - 3.68: 170 3.68 - 4.91: 25 4.91 - 6.14: 18 Bond angle restraints: 34037 Sorted by residual: angle pdb=" CD2 TRP B 631 " pdb=" CE3 TRP B 631 " pdb=" CZ3 TRP B 631 " ideal model delta sigma weight residual 118.60 124.03 -5.43 1.30e+00 5.92e-01 1.75e+01 angle pdb=" CD2 TRP C 631 " pdb=" CE3 TRP C 631 " pdb=" CZ3 TRP C 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP G 631 " pdb=" CE3 TRP G 631 " pdb=" CZ3 TRP G 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP E 631 " pdb=" CE3 TRP E 631 " pdb=" CZ3 TRP E 631 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CD2 TRP D 631 " pdb=" CE3 TRP D 631 " pdb=" CZ3 TRP D 631 " ideal model delta sigma weight residual 118.60 123.96 -5.36 1.30e+00 5.92e-01 1.70e+01 ... (remaining 34032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13837 17.87 - 35.75: 1237 35.75 - 53.62: 198 53.62 - 71.49: 43 71.49 - 89.36: 31 Dihedral angle restraints: 15346 sinusoidal: 6123 harmonic: 9223 Sorted by residual: dihedral pdb=" CA ILE A 459 " pdb=" C ILE A 459 " pdb=" N PRO A 460 " pdb=" CA PRO A 460 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ILE B 459 " pdb=" C ILE B 459 " pdb=" N PRO B 460 " pdb=" CA PRO B 460 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU C 478 " pdb=" CG GLU C 478 " pdb=" CD GLU C 478 " pdb=" OE1 GLU C 478 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2594 0.035 - 0.071: 875 0.071 - 0.106: 329 0.106 - 0.141: 129 0.141 - 0.177: 5 Chirality restraints: 3932 Sorted by residual: chirality pdb=" CB ILE A 657 " pdb=" CA ILE A 657 " pdb=" CG1 ILE A 657 " pdb=" CG2 ILE A 657 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CB ILE F 657 " pdb=" CA ILE F 657 " pdb=" CG1 ILE F 657 " pdb=" CG2 ILE F 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CB ILE D 657 " pdb=" CA ILE D 657 " pdb=" CG1 ILE D 657 " pdb=" CG2 ILE D 657 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 3929 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 268 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 269 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 459 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO E 460 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 460 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 460 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 290 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 291 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " 0.024 5.00e-02 4.00e+02 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2350 2.75 - 3.29: 23804 3.29 - 3.83: 38544 3.83 - 4.36: 47037 4.36 - 4.90: 83523 Nonbonded interactions: 195258 Sorted by model distance: nonbonded pdb=" OG1 THR G 331 " pdb=" OD2 ASP G 519 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU F 576 " pdb=" OG1 THR F 738 " model vdw 2.226 3.040 nonbonded pdb=" ND2 ASN B 485 " pdb=" O ASN B 500 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR G 220 " pdb=" OD2 ASP G 227 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 616 " pdb=" OE1 GLU A 739 " model vdw 2.255 3.040 ... (remaining 195253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'B' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'C' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'D' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'E' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'F' and (resid 216 through 449 or resid 460 through 903)) selection = (chain 'G' and (resid 216 through 321 or resid 341 through 342 or resid 356 or r \ esid 388 through 614 or (resid 615 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 616 through 742 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.060 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25224 Z= 0.124 Angle : 0.495 6.141 34037 Z= 0.293 Chirality : 0.044 0.177 3932 Planarity : 0.004 0.059 4426 Dihedral : 14.271 89.362 9308 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3163 helix: -0.87 (0.25), residues: 393 sheet: 1.49 (0.19), residues: 789 loop : -0.80 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.013 0.001 TYR A 486 PHE 0.020 0.001 PHE G 579 TRP 0.006 0.001 TRP A 502 HIS 0.000 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00243 (25224) covalent geometry : angle 0.49483 (34037) hydrogen bonds : bond 0.24830 ( 707) hydrogen bonds : angle 9.01525 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.832 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: F 402 MET cc_start: 0.7645 (ttm) cc_final: 0.7376 (ttm) REVERT: F 702 ASP cc_start: 0.7473 (t0) cc_final: 0.7151 (m-30) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.1565 time to fit residues: 71.0426 Evaluate side-chains 157 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 626 ASN B 435 ASN B 485 ASN B 686 ASN E 647 ASN F 492 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055627 restraints weight = 81766.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057351 restraints weight = 42632.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058435 restraints weight = 28870.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059072 restraints weight = 23062.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059382 restraints weight = 20330.843| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25224 Z= 0.184 Angle : 0.559 7.860 34037 Z= 0.318 Chirality : 0.046 0.216 3932 Planarity : 0.004 0.049 4426 Dihedral : 4.020 20.568 3185 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.81 % Allowed : 7.70 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3163 helix: -0.45 (0.25), residues: 400 sheet: 1.53 (0.18), residues: 790 loop : -0.77 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 667 TYR 0.013 0.001 TYR A 486 PHE 0.012 0.001 PHE F 710 TRP 0.007 0.001 TRP G 374 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00402 (25224) covalent geometry : angle 0.55948 (34037) hydrogen bonds : bond 0.04019 ( 707) hydrogen bonds : angle 6.06790 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 175 average time/residue: 0.1389 time to fit residues: 40.4030 Evaluate side-chains 157 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 704 THR Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 81 optimal weight: 5.9990 chunk 83 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 260 optimal weight: 30.0000 chunk 313 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 ASN C 431 ASN C 455 ASN F 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054263 restraints weight = 83275.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055924 restraints weight = 44519.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056963 restraints weight = 30756.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057590 restraints weight = 24815.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057945 restraints weight = 22004.360| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 25224 Z= 0.207 Angle : 0.532 5.739 34037 Z= 0.306 Chirality : 0.045 0.165 3932 Planarity : 0.004 0.046 4426 Dihedral : 4.109 20.421 3185 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.56 % Allowed : 10.24 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.14), residues: 3163 helix: -0.55 (0.24), residues: 425 sheet: 1.42 (0.18), residues: 797 loop : -0.79 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.015 0.001 TYR A 486 PHE 0.011 0.001 PHE F 710 TRP 0.008 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00462 (25224) covalent geometry : angle 0.53228 (34037) hydrogen bonds : bond 0.03636 ( 707) hydrogen bonds : angle 5.63001 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 ASN cc_start: 0.8836 (p0) cc_final: 0.8435 (t0) REVERT: C 451 MET cc_start: 0.7911 (mtt) cc_final: 0.7106 (tpp) REVERT: E 451 MET cc_start: 0.7774 (tmm) cc_final: 0.7517 (tmm) outliers start: 16 outliers final: 13 residues processed: 151 average time/residue: 0.1521 time to fit residues: 38.4525 Evaluate side-chains 148 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 704 THR Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 587 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 145 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 99 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: A 681 ASN E 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.053026 restraints weight = 83645.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054671 restraints weight = 45261.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055700 restraints weight = 31396.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056252 restraints weight = 25352.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056633 restraints weight = 22670.896| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25224 Z= 0.245 Angle : 0.558 9.548 34037 Z= 0.316 Chirality : 0.045 0.161 3932 Planarity : 0.004 0.045 4426 Dihedral : 4.299 20.843 3185 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.27 % Allowed : 11.71 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3163 helix: -0.63 (0.24), residues: 430 sheet: 1.13 (0.18), residues: 817 loop : -0.83 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 528 TYR 0.017 0.001 TYR A 486 PHE 0.013 0.001 PHE D 554 TRP 0.011 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00549 (25224) covalent geometry : angle 0.55770 (34037) hydrogen bonds : bond 0.03358 ( 707) hydrogen bonds : angle 5.44089 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7736 (mtt) cc_final: 0.7071 (tpp) REVERT: C 459 ILE cc_start: 0.8667 (tt) cc_final: 0.8456 (tt) REVERT: E 451 MET cc_start: 0.7884 (tmm) cc_final: 0.7652 (tmm) REVERT: E 740 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8449 (mm) outliers start: 36 outliers final: 23 residues processed: 161 average time/residue: 0.1394 time to fit residues: 38.3637 Evaluate side-chains 145 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 704 THR Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 587 ILE Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 59 optimal weight: 0.9990 chunk 124 optimal weight: 30.0000 chunk 197 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 734 ASN F 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053405 restraints weight = 83329.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055046 restraints weight = 44741.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056079 restraints weight = 30910.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056697 restraints weight = 24958.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.057060 restraints weight = 22128.060| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25224 Z= 0.183 Angle : 0.518 8.455 34037 Z= 0.295 Chirality : 0.044 0.155 3932 Planarity : 0.004 0.046 4426 Dihedral : 4.188 20.584 3185 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.44 % Allowed : 12.66 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3163 helix: -0.58 (0.24), residues: 430 sheet: 1.17 (0.18), residues: 822 loop : -0.78 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.012 0.001 TYR A 486 PHE 0.010 0.001 PHE G 710 TRP 0.010 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00405 (25224) covalent geometry : angle 0.51831 (34037) hydrogen bonds : bond 0.03027 ( 707) hydrogen bonds : angle 5.26637 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7719 (mtt) cc_final: 0.7252 (mmm) REVERT: C 459 ILE cc_start: 0.8558 (tt) cc_final: 0.8343 (tt) REVERT: E 451 MET cc_start: 0.7915 (tmm) cc_final: 0.7680 (tmm) REVERT: E 740 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8535 (mm) REVERT: F 303 MET cc_start: 0.7822 (tpp) cc_final: 0.7569 (tpt) outliers start: 41 outliers final: 24 residues processed: 157 average time/residue: 0.1380 time to fit residues: 36.9189 Evaluate side-chains 143 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 254 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 224 optimal weight: 40.0000 chunk 222 optimal weight: 0.0980 chunk 72 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053840 restraints weight = 83021.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055520 restraints weight = 44482.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056566 restraints weight = 30631.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057189 restraints weight = 24741.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057496 restraints weight = 21956.329| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25224 Z= 0.143 Angle : 0.505 7.873 34037 Z= 0.286 Chirality : 0.044 0.155 3932 Planarity : 0.003 0.045 4426 Dihedral : 4.041 20.148 3185 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.44 % Allowed : 13.26 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3163 helix: -0.46 (0.24), residues: 430 sheet: 1.19 (0.18), residues: 817 loop : -0.69 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.009 0.001 TYR C 486 PHE 0.008 0.001 PHE A 670 TRP 0.009 0.001 TRP F 244 HIS 0.001 0.000 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00310 (25224) covalent geometry : angle 0.50453 (34037) hydrogen bonds : bond 0.02827 ( 707) hydrogen bonds : angle 5.10093 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 451 MET cc_start: 0.7811 (mtt) cc_final: 0.7292 (mmm) REVERT: C 459 ILE cc_start: 0.8522 (tt) cc_final: 0.8295 (tt) REVERT: E 451 MET cc_start: 0.7947 (tmm) cc_final: 0.7706 (tmm) REVERT: E 740 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8527 (mm) REVERT: F 303 MET cc_start: 0.7876 (tpp) cc_final: 0.7615 (tpt) REVERT: G 304 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (mt-10) outliers start: 41 outliers final: 30 residues processed: 162 average time/residue: 0.1322 time to fit residues: 36.9660 Evaluate side-chains 152 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 chunk 68 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 282 optimal weight: 40.0000 chunk 283 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053169 restraints weight = 83682.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054802 restraints weight = 45110.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055806 restraints weight = 31221.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056438 restraints weight = 25269.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056782 restraints weight = 22426.168| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25224 Z= 0.191 Angle : 0.535 7.567 34037 Z= 0.301 Chirality : 0.045 0.190 3932 Planarity : 0.003 0.045 4426 Dihedral : 4.134 20.144 3185 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.69 % Allowed : 13.68 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3163 helix: -0.47 (0.24), residues: 430 sheet: 1.10 (0.18), residues: 817 loop : -0.73 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 457 TYR 0.013 0.001 TYR A 486 PHE 0.008 0.001 PHE F 710 TRP 0.009 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00423 (25224) covalent geometry : angle 0.53461 (34037) hydrogen bonds : bond 0.02976 ( 707) hydrogen bonds : angle 5.10298 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: C 451 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7347 (mmm) REVERT: C 459 ILE cc_start: 0.8486 (tt) cc_final: 0.8243 (tt) REVERT: C 666 LYS cc_start: 0.7306 (tptp) cc_final: 0.6989 (tptp) REVERT: E 451 MET cc_start: 0.7935 (tmm) cc_final: 0.7696 (tmm) REVERT: E 740 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (mm) REVERT: F 303 MET cc_start: 0.7952 (tpp) cc_final: 0.7719 (tpt) outliers start: 48 outliers final: 37 residues processed: 156 average time/residue: 0.1344 time to fit residues: 35.8555 Evaluate side-chains 152 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.081010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053497 restraints weight = 83497.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055147 restraints weight = 44856.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056192 restraints weight = 30951.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056814 restraints weight = 24909.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057149 restraints weight = 22096.237| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25224 Z= 0.154 Angle : 0.519 13.397 34037 Z= 0.291 Chirality : 0.044 0.160 3932 Planarity : 0.003 0.045 4426 Dihedral : 4.054 19.998 3185 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.51 % Allowed : 14.18 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3163 helix: -0.38 (0.25), residues: 430 sheet: 1.13 (0.18), residues: 817 loop : -0.68 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 667 TYR 0.010 0.001 TYR A 486 PHE 0.007 0.001 PHE G 710 TRP 0.009 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00337 (25224) covalent geometry : angle 0.51864 (34037) hydrogen bonds : bond 0.02771 ( 707) hydrogen bonds : angle 5.04188 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 739 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: C 451 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7329 (mmm) REVERT: C 459 ILE cc_start: 0.8484 (tt) cc_final: 0.8251 (tt) REVERT: C 666 LYS cc_start: 0.7521 (tptp) cc_final: 0.7118 (tptp) REVERT: E 451 MET cc_start: 0.7918 (tmm) cc_final: 0.7688 (tmm) REVERT: E 740 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (mm) REVERT: F 303 MET cc_start: 0.7989 (tpp) cc_final: 0.7732 (tpt) outliers start: 43 outliers final: 35 residues processed: 159 average time/residue: 0.1421 time to fit residues: 39.2381 Evaluate side-chains 154 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 702 ASP Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 309 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053768 restraints weight = 83356.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055427 restraints weight = 44649.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056462 restraints weight = 30767.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.057057 restraints weight = 24822.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057445 restraints weight = 22072.935| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25224 Z= 0.139 Angle : 0.511 12.377 34037 Z= 0.288 Chirality : 0.044 0.156 3932 Planarity : 0.003 0.045 4426 Dihedral : 3.999 19.590 3185 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.41 % Allowed : 14.18 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3163 helix: -0.29 (0.25), residues: 430 sheet: 1.11 (0.18), residues: 833 loop : -0.62 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 457 TYR 0.009 0.001 TYR A 486 PHE 0.007 0.001 PHE G 710 TRP 0.009 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00301 (25224) covalent geometry : angle 0.51085 (34037) hydrogen bonds : bond 0.02692 ( 707) hydrogen bonds : angle 4.94120 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 739 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: C 451 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7233 (tpp) REVERT: C 459 ILE cc_start: 0.8470 (tt) cc_final: 0.8247 (tt) REVERT: C 666 LYS cc_start: 0.7559 (tptp) cc_final: 0.7178 (tptp) REVERT: D 594 LEU cc_start: 0.8718 (tp) cc_final: 0.8503 (tt) REVERT: D 686 ASN cc_start: 0.8608 (m-40) cc_final: 0.8361 (p0) REVERT: E 451 MET cc_start: 0.7920 (tmm) cc_final: 0.7675 (tmm) REVERT: E 695 ASP cc_start: 0.8218 (t0) cc_final: 0.7859 (t0) outliers start: 40 outliers final: 35 residues processed: 159 average time/residue: 0.1429 time to fit residues: 38.8937 Evaluate side-chains 155 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 671 SER Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 255 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 214 optimal weight: 30.0000 overall best weight: 11.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 500 ASN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 734 ASN F 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051744 restraints weight = 84234.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053367 restraints weight = 45615.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054368 restraints weight = 31557.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.054982 restraints weight = 25507.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.055323 restraints weight = 22636.463| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 25224 Z= 0.308 Angle : 0.623 11.323 34037 Z= 0.344 Chirality : 0.046 0.162 3932 Planarity : 0.004 0.049 4426 Dihedral : 4.463 20.772 3185 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.55 % Allowed : 14.21 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3163 helix: -0.60 (0.24), residues: 432 sheet: 0.91 (0.18), residues: 841 loop : -0.84 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 324 TYR 0.021 0.002 TYR A 486 PHE 0.011 0.001 PHE G 731 TRP 0.010 0.001 TRP F 244 HIS 0.002 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00693 (25224) covalent geometry : angle 0.62310 (34037) hydrogen bonds : bond 0.03341 ( 707) hydrogen bonds : angle 5.24860 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: C 451 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7309 (mmm) REVERT: C 459 ILE cc_start: 0.8538 (tt) cc_final: 0.8318 (tt) REVERT: D 686 ASN cc_start: 0.8551 (m-40) cc_final: 0.8346 (p0) REVERT: E 451 MET cc_start: 0.7883 (tmm) cc_final: 0.7647 (tmm) REVERT: E 594 LEU cc_start: 0.8682 (tp) cc_final: 0.8448 (tp) outliers start: 44 outliers final: 37 residues processed: 159 average time/residue: 0.1314 time to fit residues: 36.3607 Evaluate side-chains 154 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 647 ASN Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 562 LEU Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 709 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 662 LEU Chi-restraints excluded: chain G residue 684 THR Chi-restraints excluded: chain G residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 ASN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.053026 restraints weight = 83313.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.054647 restraints weight = 44823.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055653 restraints weight = 30937.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056259 restraints weight = 24995.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056630 restraints weight = 22168.797| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25224 Z= 0.169 Angle : 0.539 11.846 34037 Z= 0.302 Chirality : 0.045 0.157 3932 Planarity : 0.003 0.048 4426 Dihedral : 4.276 20.651 3185 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.37 % Allowed : 14.49 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3163 helix: -0.50 (0.24), residues: 432 sheet: 0.92 (0.18), residues: 841 loop : -0.76 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 457 TYR 0.012 0.001 TYR A 486 PHE 0.007 0.001 PHE G 710 TRP 0.010 0.001 TRP F 244 HIS 0.001 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00376 (25224) covalent geometry : angle 0.53866 (34037) hydrogen bonds : bond 0.02892 ( 707) hydrogen bonds : angle 5.11884 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3600.77 seconds wall clock time: 63 minutes 19.16 seconds (3799.16 seconds total)