Starting phenix.real_space_refine on Sat Jun 28 07:40:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.map" model { file = "/net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds3_27682/06_2025/8ds3_27682.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.072 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 P 9 5.49 5 S 154 5.16 5 C 21312 2.51 5 N 5357 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 1.64s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32601 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "C" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 19.22, per 1000 atoms: 0.59 Number of scatterers: 32601 At special positions: 0 Unit cell: (140.432, 137.288, 194.928, 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) S 154 16.00 P 9 15.00 O 5769 8.00 N 5357 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 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: 7.63 Conformation dependent library (CDL) restraints added in 3.9 seconds 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7542 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 23 sheets defined 52.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.018A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.668A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.912A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.109A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.507A pdb=" N TRP A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.723A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.635A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 4.238A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.911A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.509A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.627A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.568A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.770A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.936A pdb=" N PHE A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.595A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.640A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.606A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.208A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.844A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.854A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 4.280A pdb=" N SER B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.532A pdb=" N ASP B 538 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.684A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.637A pdb=" N CYS B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.508A pdb=" N GLY B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.775A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.557A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.010A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.705A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.270A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 removed outlier: 3.537A pdb=" N ALA C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.068A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.634A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.755A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.247A pdb=" N PHE C 611 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.526A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.823A pdb=" N LEU C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.751A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.662A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.763A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 807 Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.254A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.565A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.653A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.942A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.006A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.761A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 343 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.005A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.589A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.056A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.702A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.629A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.560A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.344A pdb=" N VAL F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.960A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.335A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.627A pdb=" N GLU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.514A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 343 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 382 through 393 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.547A pdb=" N TRP F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.921A pdb=" N PHE F 441 " --> pdb=" O PRO F 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 443 " --> pdb=" O THR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.946A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 492 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.833A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 538 removed outlier: 3.801A pdb=" N SER F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.711A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 611 removed outlier: 4.098A pdb=" N PHE F 609 " --> pdb=" O PRO F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.524A pdb=" N SER F 632 " --> pdb=" O GLU F 629 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.934A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.699A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 745 through 749 removed outlier: 3.540A pdb=" N ILE F 748 " --> pdb=" O SER F 745 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY F 749 " --> pdb=" O PRO F 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 745 through 749' Processing helix chain 'F' and resid 768 through 772 removed outlier: 4.126A pdb=" N LEU F 771 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 772 " --> pdb=" O PRO F 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 768 through 772' Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.816A pdb=" N ALA F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.720A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.638A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA6, first strand: chain 'A' and resid 666 through 668 removed outlier: 7.012A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 735 through 737 removed outlier: 6.819A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.965A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 550 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 523 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 552 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 removed outlier: 6.611A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS C 522 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 573 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 645 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.032A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 735 through 736 removed outlier: 8.155A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.721A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.701A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 594 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS F 620 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU F 596 " --> pdb=" O LYS F 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU F 688 " --> pdb=" O SER F 712 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 457 through 458 removed outlier: 6.568A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 1439 hydrogen bonds defined for protein. 3948 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: 12.77 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6102 1.33 - 1.45: 7878 1.45 - 1.57: 19088 1.57 - 1.70: 14 1.70 - 1.82: 225 Bond restraints: 33307 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 33302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 44180 2.77 - 5.54: 628 5.54 - 8.31: 123 8.31 - 11.08: 30 11.08 - 13.85: 16 Bond angle restraints: 44977 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 44972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 19657 35.96 - 71.93: 559 71.93 - 107.89: 33 107.89 - 143.85: 14 143.85 - 179.82: 16 Dihedral angle restraints: 20279 sinusoidal: 8697 harmonic: 11582 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 20276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4898 0.098 - 0.195: 195 0.195 - 0.293: 3 0.293 - 0.390: 3 0.390 - 0.488: 8 Chirality restraints: 5107 Sorted by residual: chirality pdb=" CB ILE A 629 " pdb=" CA ILE A 629 " pdb=" CG1 ILE A 629 " pdb=" CG2 ILE A 629 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 5104 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP A 475 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 725 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " -0.046 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3254 2.75 - 3.29: 32689 3.29 - 3.82: 56283 3.82 - 4.36: 68614 4.36 - 4.90: 113233 Nonbonded interactions: 274073 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 3.040 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 3.040 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 3.040 ... (remaining 274068 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 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 808 or resid 901 through 903)) selection = (chain 'C' and (resid 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 808 or resid 901 or (resid 902 through 903 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )))) } 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 individual isotropic 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 70.920 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 : 0.005 0.152 33324 Z= 0.270 Angle : 0.898 13.848 45011 Z= 0.459 Chirality : 0.048 0.488 5107 Planarity : 0.006 0.093 5516 Dihedral : 17.578 179.817 12686 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 18.38 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3852 helix: -0.29 (0.12), residues: 1852 sheet: -1.57 (0.29), residues: 358 loop : -1.33 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 475 HIS 0.011 0.001 HIS E 694 PHE 0.041 0.002 PHE F 488 TYR 0.053 0.002 TYR F 687 ARG 0.009 0.001 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.15472 ( 1439) hydrogen bonds : angle 6.80345 ( 3948) SS BOND : bond 0.00289 ( 17) SS BOND : angle 0.75448 ( 34) covalent geometry : bond 0.00550 (33307) covalent geometry : angle 0.89772 (44977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 333 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 438 ILE cc_start: 0.7420 (pt) cc_final: 0.7125 (pt) REVERT: F 145 TRP cc_start: 0.5443 (t60) cc_final: 0.5105 (t60) outliers start: 10 outliers final: 5 residues processed: 339 average time/residue: 0.4301 time to fit residues: 238.7324 Evaluate side-chains 297 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 292 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 324 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS C 253 HIS C 377 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 409 ASN E 532 ASN E 694 HIS F 402 GLN F 424 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.159232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110788 restraints weight = 71217.284| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.22 r_work: 0.3489 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 33324 Z= 0.279 Angle : 0.655 12.162 45011 Z= 0.336 Chirality : 0.044 0.275 5107 Planarity : 0.005 0.069 5516 Dihedral : 14.210 178.542 4689 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.44 % Allowed : 17.47 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3852 helix: 0.16 (0.12), residues: 1879 sheet: -1.52 (0.30), residues: 366 loop : -1.33 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 475 HIS 0.008 0.001 HIS E 377 PHE 0.024 0.002 PHE F 388 TYR 0.027 0.002 TYR F 511 ARG 0.010 0.001 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 1439) hydrogen bonds : angle 5.16345 ( 3948) SS BOND : bond 0.00647 ( 17) SS BOND : angle 0.89964 ( 34) covalent geometry : bond 0.00650 (33307) covalent geometry : angle 0.65502 (44977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8725 (t0) cc_final: 0.8490 (t70) REVERT: A 410 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: A 429 GLU cc_start: 0.6978 (pt0) cc_final: 0.6726 (pt0) REVERT: A 433 PHE cc_start: 0.8141 (t80) cc_final: 0.7688 (t80) REVERT: A 434 MET cc_start: 0.8156 (mpp) cc_final: 0.7324 (mpp) REVERT: A 501 LYS cc_start: 0.8973 (tttt) cc_final: 0.8653 (tptt) REVERT: B 232 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6201 (tp) REVERT: B 238 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 239 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: B 444 ASP cc_start: 0.8105 (m-30) cc_final: 0.7885 (t70) REVERT: C 265 MET cc_start: 0.8279 (tpp) cc_final: 0.7980 (tpt) REVERT: C 492 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7602 (ptp-110) REVERT: C 509 PRO cc_start: 0.8132 (Cg_endo) cc_final: 0.7868 (Cg_exo) REVERT: C 590 MET cc_start: 0.4385 (mmm) cc_final: 0.4128 (mmm) REVERT: D 159 ILE cc_start: 0.9134 (tt) cc_final: 0.8858 (pt) REVERT: D 244 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: D 309 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8457 (ttm-80) REVERT: E 29 ASP cc_start: 0.8576 (t0) cc_final: 0.8049 (m-30) REVERT: E 104 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7958 (t70) REVERT: E 235 LYS cc_start: 0.8612 (mmpt) cc_final: 0.8204 (mmtt) REVERT: E 239 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: E 263 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7776 (tp) REVERT: E 394 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8081 (mt) REVERT: E 438 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8047 (tt) REVERT: E 443 PHE cc_start: 0.7698 (m-80) cc_final: 0.7488 (m-80) REVERT: E 477 TYR cc_start: 0.7634 (m-80) cc_final: 0.7262 (m-80) REVERT: F 144 PHE cc_start: 0.8124 (t80) cc_final: 0.7864 (t80) REVERT: F 175 LEU cc_start: 0.8870 (tp) cc_final: 0.8577 (mt) REVERT: F 588 MET cc_start: 0.7771 (mmp) cc_final: 0.7013 (mmm) REVERT: F 687 TYR cc_start: 0.7798 (t80) cc_final: 0.7375 (t80) outliers start: 88 outliers final: 41 residues processed: 385 average time/residue: 0.4316 time to fit residues: 273.5536 Evaluate side-chains 334 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 449 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 294 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 185 optimal weight: 0.0980 chunk 290 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 115 optimal weight: 0.0270 chunk 352 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.161096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.115495 restraints weight = 71583.600| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.21 r_work: 0.3539 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33324 Z= 0.135 Angle : 0.553 10.990 45011 Z= 0.283 Chirality : 0.040 0.214 5107 Planarity : 0.004 0.056 5516 Dihedral : 12.710 169.337 4679 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.02 % Allowed : 18.30 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3852 helix: 0.41 (0.12), residues: 1893 sheet: -1.67 (0.28), residues: 397 loop : -1.18 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 475 HIS 0.006 0.001 HIS A 694 PHE 0.028 0.001 PHE D 324 TYR 0.035 0.001 TYR F 646 ARG 0.004 0.000 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 1439) hydrogen bonds : angle 4.78835 ( 3948) SS BOND : bond 0.00267 ( 17) SS BOND : angle 0.78805 ( 34) covalent geometry : bond 0.00303 (33307) covalent geometry : angle 0.55295 (44977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 312 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7043 (pt0) cc_final: 0.6701 (pt0) REVERT: A 433 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 434 MET cc_start: 0.8038 (mpp) cc_final: 0.7309 (mpp) REVERT: A 438 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9010 (pt) REVERT: A 471 LEU cc_start: 0.8944 (tp) cc_final: 0.8354 (pp) REVERT: A 501 LYS cc_start: 0.8817 (tttt) cc_final: 0.8482 (tptt) REVERT: A 694 HIS cc_start: 0.8159 (m170) cc_final: 0.7878 (m170) REVERT: B 232 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6329 (tp) REVERT: B 444 ASP cc_start: 0.8122 (m-30) cc_final: 0.7881 (t70) REVERT: C 265 MET cc_start: 0.7860 (tpp) cc_final: 0.7566 (tpt) REVERT: C 375 MET cc_start: 0.7160 (mtm) cc_final: 0.6938 (mtm) REVERT: C 379 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7770 (mm) REVERT: C 509 PRO cc_start: 0.8040 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: C 549 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5975 (mt) REVERT: D 95 THR cc_start: 0.8887 (m) cc_final: 0.8638 (p) REVERT: D 309 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: E 235 LYS cc_start: 0.8537 (mmpt) cc_final: 0.8051 (mmtt) REVERT: E 239 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: E 263 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7762 (tp) REVERT: E 275 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8208 (t80) REVERT: E 438 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8079 (tp) REVERT: E 532 ASN cc_start: 0.5718 (m-40) cc_final: 0.5401 (m-40) REVERT: F 144 PHE cc_start: 0.7973 (t80) cc_final: 0.7738 (t80) REVERT: F 175 LEU cc_start: 0.8735 (tp) cc_final: 0.8518 (mt) REVERT: F 409 TRP cc_start: 0.6375 (m100) cc_final: 0.6037 (m100) REVERT: F 480 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8457 (mmtm) REVERT: F 503 MET cc_start: 0.8085 (mmt) cc_final: 0.7138 (tpp) REVERT: F 588 MET cc_start: 0.7543 (mmp) cc_final: 0.6876 (mmm) REVERT: F 687 TYR cc_start: 0.7891 (t80) cc_final: 0.7473 (t80) REVERT: F 735 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7334 (mtmm) outliers start: 73 outliers final: 35 residues processed: 372 average time/residue: 0.4324 time to fit residues: 261.6265 Evaluate side-chains 335 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 201 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN C 408 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.159514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110954 restraints weight = 71095.643| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.66 r_work: 0.3532 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33324 Z= 0.201 Angle : 0.568 10.031 45011 Z= 0.291 Chirality : 0.041 0.175 5107 Planarity : 0.004 0.057 5516 Dihedral : 12.212 171.601 4679 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.10 % Allowed : 18.38 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3852 helix: 0.44 (0.12), residues: 1887 sheet: -1.70 (0.28), residues: 407 loop : -1.16 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 509 HIS 0.006 0.001 HIS E 377 PHE 0.023 0.002 PHE D 324 TYR 0.017 0.002 TYR F 511 ARG 0.004 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1439) hydrogen bonds : angle 4.71342 ( 3948) SS BOND : bond 0.00443 ( 17) SS BOND : angle 0.83825 ( 34) covalent geometry : bond 0.00467 (33307) covalent geometry : angle 0.56765 (44977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 304 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.8003 (ptt-90) REVERT: A 429 GLU cc_start: 0.7053 (pt0) cc_final: 0.6827 (pt0) REVERT: A 433 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 434 MET cc_start: 0.8256 (mpp) cc_final: 0.7535 (mpp) REVERT: A 438 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8984 (pt) REVERT: A 501 LYS cc_start: 0.8832 (tttt) cc_final: 0.8504 (tptt) REVERT: B 46 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: B 232 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6503 (tp) REVERT: B 239 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: C 235 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8567 (tppp) REVERT: C 265 MET cc_start: 0.8169 (tpp) cc_final: 0.7827 (tpt) REVERT: C 375 MET cc_start: 0.7390 (mtm) cc_final: 0.7134 (mtm) REVERT: C 379 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 509 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7899 (Cg_exo) REVERT: D 95 THR cc_start: 0.9010 (m) cc_final: 0.8755 (p) REVERT: D 159 ILE cc_start: 0.9119 (tt) cc_final: 0.8872 (pt) REVERT: E 29 ASP cc_start: 0.8513 (t0) cc_final: 0.8022 (m-30) REVERT: E 104 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7898 (t70) REVERT: E 160 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8700 (tt) REVERT: E 235 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8139 (mmtt) REVERT: E 239 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: E 263 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7707 (tp) REVERT: E 477 TYR cc_start: 0.7748 (m-80) cc_final: 0.7103 (m-80) REVERT: E 532 ASN cc_start: 0.5899 (m-40) cc_final: 0.5689 (m-40) REVERT: E 673 LYS cc_start: 0.7672 (mppt) cc_final: 0.7298 (mmtm) REVERT: F 144 PHE cc_start: 0.8159 (t80) cc_final: 0.7884 (t80) REVERT: F 175 LEU cc_start: 0.8800 (tp) cc_final: 0.8599 (mt) REVERT: F 409 TRP cc_start: 0.6493 (m100) cc_final: 0.6131 (m100) REVERT: F 503 MET cc_start: 0.8034 (mmt) cc_final: 0.7164 (tpp) REVERT: F 588 MET cc_start: 0.7558 (mmp) cc_final: 0.6867 (mmm) REVERT: F 687 TYR cc_start: 0.8047 (t80) cc_final: 0.7726 (t80) outliers start: 112 outliers final: 58 residues processed: 399 average time/residue: 0.4496 time to fit residues: 292.4431 Evaluate side-chains 355 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 749 ARG Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 147 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 342 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.160475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.113376 restraints weight = 71347.407| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.27 r_work: 0.3509 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33324 Z= 0.141 Angle : 0.535 9.939 45011 Z= 0.274 Chirality : 0.040 0.202 5107 Planarity : 0.004 0.058 5516 Dihedral : 11.591 179.034 4679 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.74 % Allowed : 18.96 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3852 helix: 0.57 (0.12), residues: 1893 sheet: -1.76 (0.27), residues: 423 loop : -1.09 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP F 509 HIS 0.009 0.001 HIS E 694 PHE 0.022 0.001 PHE F 488 TYR 0.036 0.001 TYR F 646 ARG 0.005 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 1439) hydrogen bonds : angle 4.57055 ( 3948) SS BOND : bond 0.00277 ( 17) SS BOND : angle 0.75991 ( 34) covalent geometry : bond 0.00321 (33307) covalent geometry : angle 0.53486 (44977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 301 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.7053 (pt0) cc_final: 0.6748 (pt0) REVERT: A 433 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7508 (t80) REVERT: A 434 MET cc_start: 0.8183 (mpp) cc_final: 0.7368 (mpp) REVERT: A 438 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8972 (pt) REVERT: A 471 LEU cc_start: 0.8966 (tp) cc_final: 0.8276 (pp) REVERT: A 501 LYS cc_start: 0.8770 (tttt) cc_final: 0.8443 (tptt) REVERT: B 46 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: B 232 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6587 (tp) REVERT: B 239 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: B 434 MET cc_start: 0.5989 (mmt) cc_final: 0.5651 (mmt) REVERT: C 235 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8549 (tppp) REVERT: C 265 MET cc_start: 0.7849 (tpp) cc_final: 0.7545 (tpt) REVERT: C 337 MET cc_start: 0.8745 (mmm) cc_final: 0.8545 (mmm) REVERT: C 375 MET cc_start: 0.7080 (mtm) cc_final: 0.6851 (mtm) REVERT: C 379 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7915 (mm) REVERT: C 509 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7914 (Cg_exo) REVERT: D 95 THR cc_start: 0.8920 (m) cc_final: 0.8690 (p) REVERT: D 159 ILE cc_start: 0.9164 (tt) cc_final: 0.8915 (pt) REVERT: E 263 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7734 (tp) REVERT: E 275 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8305 (t80) REVERT: E 394 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7877 (mt) REVERT: E 477 TYR cc_start: 0.7683 (m-80) cc_final: 0.7189 (m-80) REVERT: E 694 HIS cc_start: 0.6771 (t-170) cc_final: 0.6467 (t-170) REVERT: F 144 PHE cc_start: 0.8045 (t80) cc_final: 0.7827 (t80) REVERT: F 409 TRP cc_start: 0.6433 (m100) cc_final: 0.6100 (m100) REVERT: F 458 MET cc_start: 0.8316 (tpt) cc_final: 0.8096 (tpt) REVERT: F 503 MET cc_start: 0.7963 (mmt) cc_final: 0.7111 (tpp) REVERT: F 545 LYS cc_start: 0.7472 (mmtt) cc_final: 0.6250 (tttm) REVERT: F 588 MET cc_start: 0.7518 (mmp) cc_final: 0.6882 (mmm) REVERT: F 687 TYR cc_start: 0.8057 (t80) cc_final: 0.7788 (t80) outliers start: 99 outliers final: 71 residues processed: 384 average time/residue: 0.4544 time to fit residues: 283.1732 Evaluate side-chains 366 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 208 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 324 optimal weight: 0.9990 chunk 333 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 383 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN C 408 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN F 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.160324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.114532 restraints weight = 69965.617| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.11 r_work: 0.3543 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33324 Z= 0.124 Angle : 0.525 11.320 45011 Z= 0.267 Chirality : 0.040 0.175 5107 Planarity : 0.004 0.062 5516 Dihedral : 10.900 170.293 4679 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.69 % Allowed : 19.21 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3852 helix: 0.65 (0.12), residues: 1895 sheet: -1.58 (0.28), residues: 424 loop : -1.09 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP F 509 HIS 0.007 0.001 HIS F 482 PHE 0.019 0.001 PHE F 342 TYR 0.018 0.001 TYR F 511 ARG 0.005 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1439) hydrogen bonds : angle 4.45206 ( 3948) SS BOND : bond 0.00265 ( 17) SS BOND : angle 0.73946 ( 34) covalent geometry : bond 0.00283 (33307) covalent geometry : angle 0.52492 (44977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 307 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7545 (t80) REVERT: A 434 MET cc_start: 0.8255 (mpp) cc_final: 0.7366 (mpp) REVERT: A 438 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8977 (pt) REVERT: A 471 LEU cc_start: 0.8992 (tp) cc_final: 0.8324 (pp) REVERT: A 501 LYS cc_start: 0.8852 (tttt) cc_final: 0.8532 (tptt) REVERT: A 694 HIS cc_start: 0.8225 (m170) cc_final: 0.8003 (m170) REVERT: B 46 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7417 (tp40) REVERT: B 232 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6666 (tp) REVERT: B 239 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: B 375 MET cc_start: 0.7114 (mtm) cc_final: 0.6849 (mtm) REVERT: B 434 MET cc_start: 0.6068 (mmt) cc_final: 0.5694 (mmt) REVERT: C 235 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8590 (tppp) REVERT: C 265 MET cc_start: 0.8107 (tpp) cc_final: 0.7802 (tpt) REVERT: C 379 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8081 (mm) REVERT: C 492 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7520 (ptp-170) REVERT: C 509 PRO cc_start: 0.8135 (Cg_endo) cc_final: 0.7886 (Cg_exo) REVERT: D 95 THR cc_start: 0.9008 (m) cc_final: 0.8759 (p) REVERT: D 159 ILE cc_start: 0.9115 (tt) cc_final: 0.8859 (pt) REVERT: E 263 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7736 (tp) REVERT: E 275 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8253 (t80) REVERT: E 394 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8025 (mt) REVERT: E 477 TYR cc_start: 0.7850 (m-80) cc_final: 0.7359 (m-80) REVERT: E 660 ASN cc_start: 0.8014 (m-40) cc_final: 0.7636 (p0) REVERT: E 673 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7025 (mmtm) REVERT: F 144 PHE cc_start: 0.8084 (t80) cc_final: 0.7706 (t80) REVERT: F 409 TRP cc_start: 0.6399 (m100) cc_final: 0.6072 (m100) REVERT: F 503 MET cc_start: 0.7979 (mmt) cc_final: 0.7116 (tpp) REVERT: F 545 LYS cc_start: 0.7493 (mmtt) cc_final: 0.6324 (tttm) REVERT: F 581 MET cc_start: 0.5761 (tpt) cc_final: 0.5506 (tpt) REVERT: F 588 MET cc_start: 0.7496 (mmp) cc_final: 0.6868 (mmm) REVERT: F 615 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6843 (tp-100) REVERT: F 687 TYR cc_start: 0.8059 (t80) cc_final: 0.7734 (t80) outliers start: 97 outliers final: 62 residues processed: 385 average time/residue: 0.4536 time to fit residues: 284.4887 Evaluate side-chains 367 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 295 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 217 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 239 optimal weight: 0.2980 chunk 232 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 332 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.160109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.112253 restraints weight = 68884.985| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.15 r_work: 0.3453 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33324 Z= 0.135 Angle : 0.530 11.018 45011 Z= 0.269 Chirality : 0.040 0.244 5107 Planarity : 0.004 0.064 5516 Dihedral : 10.419 164.804 4679 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.91 % Allowed : 19.24 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3852 helix: 0.63 (0.12), residues: 1909 sheet: -1.56 (0.28), residues: 430 loop : -1.06 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP F 509 HIS 0.010 0.001 HIS E 694 PHE 0.018 0.001 PHE E 490 TYR 0.029 0.001 TYR F 646 ARG 0.004 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1439) hydrogen bonds : angle 4.40600 ( 3948) SS BOND : bond 0.00289 ( 17) SS BOND : angle 0.77177 ( 34) covalent geometry : bond 0.00311 (33307) covalent geometry : angle 0.53014 (44977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 304 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7464 (t80) REVERT: A 434 MET cc_start: 0.8248 (mpp) cc_final: 0.7282 (mpp) REVERT: A 471 LEU cc_start: 0.8946 (tp) cc_final: 0.8315 (pp) REVERT: A 501 LYS cc_start: 0.8794 (tttt) cc_final: 0.8475 (tptt) REVERT: A 557 LYS cc_start: 0.7884 (pttp) cc_final: 0.7517 (pptt) REVERT: A 623 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: A 694 HIS cc_start: 0.8269 (m170) cc_final: 0.8012 (m170) REVERT: A 708 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7221 (tp-100) REVERT: B 46 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7254 (tp40) REVERT: B 232 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6808 (tp) REVERT: B 239 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: B 375 MET cc_start: 0.7106 (mtm) cc_final: 0.6852 (mtm) REVERT: B 434 MET cc_start: 0.6186 (mmt) cc_final: 0.5799 (mmt) REVERT: B 468 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7117 (tp) REVERT: B 471 LEU cc_start: 0.8882 (tp) cc_final: 0.8366 (mt) REVERT: C 265 MET cc_start: 0.7839 (tpp) cc_final: 0.7530 (tpt) REVERT: C 379 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7936 (mm) REVERT: D 95 THR cc_start: 0.8982 (m) cc_final: 0.8709 (p) REVERT: D 244 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: E 104 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7794 (t70) REVERT: E 233 ASP cc_start: 0.8331 (m-30) cc_final: 0.7843 (t0) REVERT: E 263 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7591 (tp) REVERT: E 275 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8207 (t80) REVERT: E 477 TYR cc_start: 0.7905 (m-80) cc_final: 0.7445 (m-80) REVERT: E 660 ASN cc_start: 0.8089 (m-40) cc_final: 0.7687 (p0) REVERT: E 673 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7082 (mmtm) REVERT: F 144 PHE cc_start: 0.8011 (t80) cc_final: 0.7266 (t80) REVERT: F 148 PHE cc_start: 0.7207 (t80) cc_final: 0.6854 (m-80) REVERT: F 409 TRP cc_start: 0.6368 (m100) cc_final: 0.6037 (m100) REVERT: F 503 MET cc_start: 0.7999 (mmt) cc_final: 0.7133 (tpp) REVERT: F 545 LYS cc_start: 0.7494 (mmtt) cc_final: 0.6484 (tttp) REVERT: F 588 MET cc_start: 0.7571 (mmp) cc_final: 0.7071 (mmm) REVERT: F 615 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6912 (tp-100) outliers start: 105 outliers final: 66 residues processed: 392 average time/residue: 0.4649 time to fit residues: 294.8351 Evaluate side-chains 368 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 109 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 320 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 342 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 287 optimal weight: 0.4980 chunk 149 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.160328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.112535 restraints weight = 68954.265| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.20 r_work: 0.3464 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33324 Z= 0.121 Angle : 0.534 12.043 45011 Z= 0.269 Chirality : 0.040 0.407 5107 Planarity : 0.004 0.058 5516 Dihedral : 9.914 158.154 4679 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.46 % Allowed : 19.57 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3852 helix: 0.71 (0.12), residues: 1906 sheet: -1.48 (0.28), residues: 423 loop : -1.02 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 509 HIS 0.007 0.001 HIS E 694 PHE 0.015 0.001 PHE D 324 TYR 0.017 0.001 TYR D 285 ARG 0.005 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 1439) hydrogen bonds : angle 4.36699 ( 3948) SS BOND : bond 0.00269 ( 17) SS BOND : angle 0.74129 ( 34) covalent geometry : bond 0.00276 (33307) covalent geometry : angle 0.53342 (44977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: A 433 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7463 (t80) REVERT: A 434 MET cc_start: 0.8325 (mpp) cc_final: 0.7436 (mpp) REVERT: A 471 LEU cc_start: 0.8958 (tp) cc_final: 0.8337 (pp) REVERT: A 501 LYS cc_start: 0.8741 (tttt) cc_final: 0.8390 (tptt) REVERT: A 557 LYS cc_start: 0.7736 (pttp) cc_final: 0.7423 (pptt) REVERT: A 623 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: A 624 ASN cc_start: 0.7838 (m110) cc_final: 0.7612 (m110) REVERT: A 694 HIS cc_start: 0.8332 (m170) cc_final: 0.8111 (m170) REVERT: B 46 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7234 (tp40) REVERT: B 232 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6832 (tp) REVERT: B 236 GLU cc_start: 0.8195 (tt0) cc_final: 0.7772 (tm-30) REVERT: B 239 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: B 298 ASP cc_start: 0.7576 (t0) cc_final: 0.7318 (t0) REVERT: B 375 MET cc_start: 0.7086 (mtm) cc_final: 0.6825 (mtm) REVERT: B 434 MET cc_start: 0.6078 (mmt) cc_final: 0.5714 (mmt) REVERT: B 468 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7109 (tp) REVERT: B 471 LEU cc_start: 0.8899 (tp) cc_final: 0.8386 (mt) REVERT: C 265 MET cc_start: 0.7807 (tpp) cc_final: 0.7505 (tpt) REVERT: C 379 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7928 (mm) REVERT: C 492 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.7367 (ptp-170) REVERT: C 509 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.8029 (Cg_exo) REVERT: D 95 THR cc_start: 0.8963 (m) cc_final: 0.8618 (p) REVERT: D 244 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.5921 (m-80) REVERT: E 263 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7569 (tp) REVERT: E 275 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8036 (t80) REVERT: E 477 TYR cc_start: 0.7946 (m-80) cc_final: 0.7558 (m-10) REVERT: E 660 ASN cc_start: 0.8053 (m-40) cc_final: 0.7653 (p0) REVERT: E 673 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7034 (mmtm) REVERT: F 144 PHE cc_start: 0.7955 (t80) cc_final: 0.7271 (t80) REVERT: F 148 PHE cc_start: 0.7226 (t80) cc_final: 0.6907 (m-80) REVERT: F 175 LEU cc_start: 0.7922 (mm) cc_final: 0.7641 (tt) REVERT: F 409 TRP cc_start: 0.6342 (m100) cc_final: 0.6025 (m100) REVERT: F 503 MET cc_start: 0.7981 (mmt) cc_final: 0.7091 (tpp) REVERT: F 545 LYS cc_start: 0.7515 (mmtt) cc_final: 0.6473 (tttm) REVERT: F 588 MET cc_start: 0.7672 (mmp) cc_final: 0.7162 (mmm) REVERT: F 590 ASN cc_start: 0.8105 (m-40) cc_final: 0.7834 (m110) REVERT: F 615 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6922 (tp-100) outliers start: 89 outliers final: 61 residues processed: 387 average time/residue: 0.4495 time to fit residues: 282.5464 Evaluate side-chains 369 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 759 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 0.0000 chunk 25 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 292 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 574 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.160399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114140 restraints weight = 68953.839| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.06 r_work: 0.3470 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33324 Z= 0.121 Angle : 0.534 10.726 45011 Z= 0.269 Chirality : 0.040 0.401 5107 Planarity : 0.004 0.060 5516 Dihedral : 9.502 151.597 4679 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.33 % Allowed : 19.66 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3852 helix: 0.73 (0.12), residues: 1907 sheet: -1.45 (0.28), residues: 423 loop : -0.99 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 509 HIS 0.013 0.001 HIS E 694 PHE 0.019 0.001 PHE E 490 TYR 0.019 0.001 TYR D 325 ARG 0.005 0.000 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1439) hydrogen bonds : angle 4.33320 ( 3948) SS BOND : bond 0.00268 ( 17) SS BOND : angle 0.77420 ( 34) covalent geometry : bond 0.00278 (33307) covalent geometry : angle 0.53347 (44977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 304 time to evaluate : 6.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: A 433 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7408 (t80) REVERT: A 434 MET cc_start: 0.8279 (mpp) cc_final: 0.7358 (mpp) REVERT: A 471 LEU cc_start: 0.8965 (tp) cc_final: 0.8317 (pp) REVERT: A 501 LYS cc_start: 0.8773 (tttt) cc_final: 0.8411 (tptt) REVERT: A 557 LYS cc_start: 0.7778 (pttp) cc_final: 0.7456 (pptt) REVERT: A 597 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7237 (mp0) REVERT: A 623 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: A 624 ASN cc_start: 0.7899 (m110) cc_final: 0.7648 (m110) REVERT: A 694 HIS cc_start: 0.8367 (m170) cc_final: 0.8116 (m170) REVERT: A 708 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7235 (tp-100) REVERT: B 46 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: B 232 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6825 (tp) REVERT: B 239 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: B 375 MET cc_start: 0.6983 (mtm) cc_final: 0.6721 (mtm) REVERT: B 434 MET cc_start: 0.6104 (mmt) cc_final: 0.5767 (mmt) REVERT: B 468 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7198 (tp) REVERT: B 471 LEU cc_start: 0.8906 (tp) cc_final: 0.8387 (mt) REVERT: C 379 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7986 (mm) REVERT: D 95 THR cc_start: 0.8950 (m) cc_final: 0.8623 (p) REVERT: D 159 ILE cc_start: 0.9103 (tt) cc_final: 0.8831 (pt) REVERT: D 244 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: D 325 TYR cc_start: 0.8192 (t80) cc_final: 0.7951 (t80) REVERT: E 263 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7679 (tp) REVERT: E 275 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8080 (t80) REVERT: E 394 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7947 (mt) REVERT: E 477 TYR cc_start: 0.7944 (m-80) cc_final: 0.7591 (m-80) REVERT: E 660 ASN cc_start: 0.8061 (m-40) cc_final: 0.7631 (p0) REVERT: E 673 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7058 (mmtm) REVERT: F 144 PHE cc_start: 0.7879 (t80) cc_final: 0.7286 (t80) REVERT: F 148 PHE cc_start: 0.7119 (t80) cc_final: 0.6848 (m-80) REVERT: F 409 TRP cc_start: 0.6334 (m100) cc_final: 0.6015 (m100) REVERT: F 503 MET cc_start: 0.7928 (mmt) cc_final: 0.6936 (tpp) REVERT: F 545 LYS cc_start: 0.7551 (mmtt) cc_final: 0.6531 (tttm) REVERT: F 546 ILE cc_start: 0.7296 (mt) cc_final: 0.7025 (mt) REVERT: F 588 MET cc_start: 0.7602 (mmp) cc_final: 0.7119 (mmm) REVERT: F 590 ASN cc_start: 0.8159 (m-40) cc_final: 0.7883 (m110) REVERT: F 615 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6955 (tp-100) outliers start: 84 outliers final: 60 residues processed: 375 average time/residue: 0.5332 time to fit residues: 327.7179 Evaluate side-chains 369 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 198 optimal weight: 0.0570 chunk 119 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 375 optimal weight: 0.0060 chunk 83 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 312 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.160644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113640 restraints weight = 69111.650| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.17 r_work: 0.3484 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33324 Z= 0.113 Angle : 0.535 11.537 45011 Z= 0.269 Chirality : 0.040 0.386 5107 Planarity : 0.004 0.060 5516 Dihedral : 9.007 141.650 4679 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.02 % Allowed : 19.99 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3852 helix: 0.77 (0.12), residues: 1908 sheet: -1.29 (0.29), residues: 408 loop : -1.00 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 511 HIS 0.011 0.001 HIS E 694 PHE 0.018 0.001 PHE E 250 TYR 0.017 0.001 TYR D 325 ARG 0.010 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1439) hydrogen bonds : angle 4.28665 ( 3948) SS BOND : bond 0.00244 ( 17) SS BOND : angle 0.75910 ( 34) covalent geometry : bond 0.00257 (33307) covalent geometry : angle 0.53488 (44977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 434 MET cc_start: 0.8288 (mpp) cc_final: 0.7370 (mpp) REVERT: A 471 LEU cc_start: 0.8959 (tp) cc_final: 0.8305 (pp) REVERT: A 501 LYS cc_start: 0.8615 (tttt) cc_final: 0.8277 (tptt) REVERT: A 557 LYS cc_start: 0.7776 (pttp) cc_final: 0.7447 (pptt) REVERT: A 597 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7207 (mp0) REVERT: A 623 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: A 624 ASN cc_start: 0.7898 (m110) cc_final: 0.7626 (m110) REVERT: A 694 HIS cc_start: 0.8393 (m170) cc_final: 0.8146 (m170) REVERT: A 708 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7208 (tp-100) REVERT: B 46 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7249 (tp40) REVERT: B 115 GLU cc_start: 0.8215 (tp30) cc_final: 0.7967 (tp30) REVERT: B 232 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6849 (tp) REVERT: B 236 GLU cc_start: 0.8157 (tt0) cc_final: 0.7779 (tm-30) REVERT: B 239 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: B 375 MET cc_start: 0.7094 (mtm) cc_final: 0.6840 (mtm) REVERT: B 434 MET cc_start: 0.6221 (mmt) cc_final: 0.5836 (mmt) REVERT: B 471 LEU cc_start: 0.8917 (tp) cc_final: 0.8413 (mt) REVERT: B 644 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5862 (tp) REVERT: C 379 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (mm) REVERT: D 95 THR cc_start: 0.8963 (m) cc_final: 0.8608 (p) REVERT: E 263 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7624 (tp) REVERT: E 275 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7869 (t80) REVERT: E 394 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (mt) REVERT: E 477 TYR cc_start: 0.7985 (m-80) cc_final: 0.7628 (m-80) REVERT: E 660 ASN cc_start: 0.8082 (m-40) cc_final: 0.7640 (p0) REVERT: E 673 LYS cc_start: 0.7554 (mmtt) cc_final: 0.7026 (mmtm) REVERT: F 144 PHE cc_start: 0.7837 (t80) cc_final: 0.7268 (t80) REVERT: F 148 PHE cc_start: 0.7061 (t80) cc_final: 0.6819 (m-80) REVERT: F 409 TRP cc_start: 0.6408 (m100) cc_final: 0.6077 (m100) REVERT: F 503 MET cc_start: 0.7546 (mmt) cc_final: 0.7245 (tpp) REVERT: F 545 LYS cc_start: 0.7586 (mmtt) cc_final: 0.6623 (tttm) REVERT: F 546 ILE cc_start: 0.7232 (mt) cc_final: 0.6956 (mt) REVERT: F 588 MET cc_start: 0.7606 (mmp) cc_final: 0.7129 (mmm) REVERT: F 590 ASN cc_start: 0.8193 (m-40) cc_final: 0.7920 (m110) REVERT: F 615 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6931 (tp-100) outliers start: 73 outliers final: 56 residues processed: 373 average time/residue: 0.4390 time to fit residues: 266.5952 Evaluate side-chains 362 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 294 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 55 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 229 optimal weight: 0.0770 chunk 248 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 196 optimal weight: 0.0020 chunk 256 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 361 optimal weight: 0.0070 overall best weight: 0.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.161723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.114260 restraints weight = 68954.043| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.24 r_work: 0.3505 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33324 Z= 0.097 Angle : 0.526 11.470 45011 Z= 0.263 Chirality : 0.040 0.388 5107 Planarity : 0.004 0.059 5516 Dihedral : 8.474 133.228 4679 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.77 % Allowed : 20.49 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3852 helix: 0.88 (0.12), residues: 1893 sheet: -1.20 (0.28), residues: 416 loop : -0.94 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 511 HIS 0.010 0.001 HIS E 694 PHE 0.052 0.001 PHE E 250 TYR 0.031 0.001 TYR D 325 ARG 0.004 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 1439) hydrogen bonds : angle 4.19223 ( 3948) SS BOND : bond 0.00216 ( 17) SS BOND : angle 0.72931 ( 34) covalent geometry : bond 0.00212 (33307) covalent geometry : angle 0.52570 (44977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25817.76 seconds wall clock time: 448 minutes 15.85 seconds (26895.85 seconds total)