Starting phenix.real_space_refine on Thu May 22 03:08:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6o_42998/05_2025/8v6o_42998.cif" } resolution = 2.83 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= 0.004 sd= 0.050 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Na 3 4.78 5 B 8 2.79 5 C 15000 2.51 5 N 3496 2.21 5 O 4016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22683 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5209 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 504 Unusual residues: {' NA': 2, 'FZ4': 2, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 450 Unusual residues: {'FZ4': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 398 Unusual residues: {'FZ4': 2, 'POV': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 451 Unusual residues: {' NA': 1, 'FZ4': 2, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 12.39, per 1000 atoms: 0.55 Number of scatterers: 22683 At special positions: 0 Unit cell: (156.8, 156, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 32 15.00 Na 3 11.00 O 4016 8.00 N 3496 7.00 C 15000 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.02 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 64.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.586A pdb=" N LYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.975A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.748A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.612A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.586A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.519A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.526A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 505 removed outlier: 3.503A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 4.057A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.593A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.578A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS A 614 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 615 " --> pdb=" O CYS A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 611 through 615' Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.593A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.703A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.523A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.976A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.747A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.692A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.600A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.587A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.548A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.519A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 505 removed outlier: 3.502A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 4.057A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.593A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.578A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS B 614 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 615 " --> pdb=" O CYS B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 615' Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.592A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.703A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.523A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.613A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.975A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.524A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.747A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.587A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.644A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.500A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.518A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 505 removed outlier: 3.503A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 4.056A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.594A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.579A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS C 614 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 615 " --> pdb=" O CYS C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 611 through 615' Processing helix chain 'C' and resid 623 through 638 removed outlier: 3.592A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 707 removed outlier: 3.952A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.704A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.524A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.614A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.976A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.525A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.748A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.691A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.599A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.613A pdb=" N ALA D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.588A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.645A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.500A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.658A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.518A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.529A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.580A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.527A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 505 removed outlier: 3.502A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.836A pdb=" N ASP D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 4.056A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.594A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.579A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 606 removed outlier: 3.732A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.721A pdb=" N LYS D 614 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 615 " --> pdb=" O CYS D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 611 through 615' Processing helix chain 'D' and resid 623 through 638 removed outlier: 3.593A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 650 through 677 removed outlier: 3.725A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 707 removed outlier: 3.951A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.704A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.111A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.112A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2778 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: 6.08 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3416 1.31 - 1.44: 6092 1.44 - 1.56: 13276 1.56 - 1.69: 80 1.69 - 1.81: 212 Bond restraints: 23076 Sorted by residual: bond pdb=" C21 POV D 904 " pdb=" O21 POV D 904 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C21 POV A 911 " pdb=" O21 POV A 911 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV C 901 " pdb=" O21 POV C 901 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 23071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 29761 2.84 - 5.68: 722 5.68 - 8.51: 264 8.51 - 11.35: 99 11.35 - 14.19: 42 Bond angle restraints: 30888 Sorted by residual: angle pdb=" C LYS A 611 " pdb=" N CYS A 612 " pdb=" CA CYS A 612 " ideal model delta sigma weight residual 120.58 127.05 -6.47 1.32e+00 5.74e-01 2.41e+01 angle pdb=" C LYS C 611 " pdb=" N CYS C 612 " pdb=" CA CYS C 612 " ideal model delta sigma weight residual 120.58 127.02 -6.44 1.32e+00 5.74e-01 2.38e+01 angle pdb=" C LYS D 611 " pdb=" N CYS D 612 " pdb=" CA CYS D 612 " ideal model delta sigma weight residual 120.58 127.02 -6.44 1.32e+00 5.74e-01 2.38e+01 angle pdb=" C LYS B 611 " pdb=" N CYS B 612 " pdb=" CA CYS B 612 " ideal model delta sigma weight residual 120.58 127.00 -6.42 1.32e+00 5.74e-01 2.37e+01 angle pdb=" O11 POV D 908 " pdb=" P POV D 908 " pdb=" O12 POV D 908 " ideal model delta sigma weight residual 97.67 111.86 -14.19 3.00e+00 1.11e-01 2.24e+01 ... (remaining 30883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 13434 35.31 - 70.62: 594 70.62 - 105.94: 72 105.94 - 141.25: 47 141.25 - 176.56: 9 Dihedral angle restraints: 14156 sinusoidal: 6612 harmonic: 7544 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.10 -59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.08 -59.08 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual 93.00 152.07 -59.07 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 14153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2155 0.035 - 0.069: 763 0.069 - 0.104: 305 0.104 - 0.139: 59 0.139 - 0.173: 26 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA PRO D 613 " pdb=" N PRO D 613 " pdb=" C PRO D 613 " pdb=" CB PRO D 613 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C2 POV C 901 " pdb=" C1 POV C 901 " pdb=" C3 POV C 901 " pdb=" O21 POV C 901 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA PRO A 613 " pdb=" N PRO A 613 " pdb=" C PRO A 613 " pdb=" CB PRO A 613 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 3305 not shown) Planarity restraints: 3716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 462 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 463 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 462 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO C 463 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 462 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO D 463 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.033 5.00e-02 4.00e+02 ... (remaining 3713 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6217 2.81 - 3.33: 18557 3.33 - 3.86: 35233 3.86 - 4.38: 43074 4.38 - 4.90: 73203 Nonbonded interactions: 176284 Sorted by model distance: nonbonded pdb=" O PRO C 753 " pdb=" OH TYR D 213 " model vdw 2.290 3.040 nonbonded pdb=" O HIS B 417 " pdb=" OG1 THR B 421 " model vdw 2.294 3.040 nonbonded pdb=" O HIS C 417 " pdb=" OG1 THR C 421 " model vdw 2.295 3.040 nonbonded pdb=" O HIS A 417 " pdb=" OG1 THR A 421 " model vdw 2.295 3.040 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.295 3.040 ... (remaining 176279 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 117 through 756 or resid 901 through 905)) selection = (chain 'B' and (resid 117 through 756 or resid 901 through 905)) selection = (chain 'C' and (resid 117 through 756 or resid 901 through 905)) selection = (chain 'D' and (resid 117 through 756 or resid 901 through 905)) } 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=0.45 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.470 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.009 0.100 23080 Z= 0.472 Angle : 1.361 14.190 30896 Z= 0.640 Chirality : 0.043 0.173 3308 Planarity : 0.006 0.060 3716 Dihedral : 20.284 176.559 9248 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.47 % 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: -6.54 (0.09), residues: 2552 helix: -4.73 (0.04), residues: 1576 sheet: -1.03 (0.41), residues: 112 loop : -3.55 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 692 HIS 0.008 0.002 HIS C 471 PHE 0.023 0.002 PHE A 633 TYR 0.012 0.001 TYR A 461 ARG 0.009 0.001 ARG D 693 Details of bonding type rmsd hydrogen bonds : bond 0.34815 ( 942) hydrogen bonds : angle 9.96759 ( 2778) SS BOND : bond 0.00971 ( 4) SS BOND : angle 0.47548 ( 8) covalent geometry : bond 0.00934 (23076) covalent geometry : angle 1.36096 (30888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 574 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6981 (tmmt) REVERT: B 478 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: B 716 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7288 (tpp-160) REVERT: C 121 LYS cc_start: 0.7596 (mptt) cc_final: 0.7122 (pttm) REVERT: C 367 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7441 (pt0) REVERT: C 478 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7090 (tmmt) REVERT: C 716 ARG cc_start: 0.8008 (ttp-170) cc_final: 0.7378 (tpm170) REVERT: D 156 ASP cc_start: 0.7795 (t0) cc_final: 0.7356 (t0) REVERT: D 431 MET cc_start: 0.7045 (mtp) cc_final: 0.6665 (mmt) REVERT: D 478 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7083 (tmmt) REVERT: D 592 PHE cc_start: 0.6920 (m-10) cc_final: 0.6696 (m-10) REVERT: D 595 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7135 (mm) REVERT: D 716 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7289 (tpp-160) outliers start: 8 outliers final: 0 residues processed: 582 average time/residue: 1.3187 time to fit residues: 872.4437 Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 339 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 286 GLN A 314 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 671 ASN B 286 GLN B 314 ASN B 671 ASN C 160 HIS C 286 GLN C 314 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 251 ASN D 279 GLN D 286 GLN D 314 ASN D 580 GLN D 643 ASN D 671 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119828 restraints weight = 26559.391| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.31 r_work: 0.3216 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23080 Z= 0.214 Angle : 0.723 7.295 30896 Z= 0.360 Chirality : 0.043 0.180 3308 Planarity : 0.006 0.055 3716 Dihedral : 24.078 155.962 4226 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 3.79 % Allowed : 12.21 % Favored : 83.99 % 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: -3.30 (0.13), residues: 2552 helix: -1.84 (0.10), residues: 1588 sheet: -1.12 (0.41), residues: 112 loop : -2.76 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 692 HIS 0.010 0.002 HIS A 471 PHE 0.028 0.002 PHE B 633 TYR 0.020 0.002 TYR D 451 ARG 0.005 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 942) hydrogen bonds : angle 4.25822 ( 2778) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.28438 ( 8) covalent geometry : bond 0.00514 (23076) covalent geometry : angle 0.72298 (30888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 377 time to evaluate : 2.223 Fit side-chains REVERT: A 220 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8281 (m-40) REVERT: A 431 MET cc_start: 0.8040 (mtp) cc_final: 0.7187 (mmt) REVERT: A 478 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7148 (tmmt) REVERT: A 631 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 690 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7762 (mtm110) REVERT: A 712 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7528 (mtt90) REVERT: B 159 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6546 (mmp) REVERT: B 202 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7729 (ptm160) REVERT: B 478 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7235 (tmmt) REVERT: B 631 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 690 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7802 (mtm110) REVERT: B 716 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.7296 (tpp-160) REVERT: C 327 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7456 (mmm-85) REVERT: C 367 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7358 (pt0) REVERT: C 478 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7180 (tmmt) REVERT: C 631 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: C 712 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7783 (mtm110) REVERT: C 716 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7352 (tpm170) REVERT: D 156 ASP cc_start: 0.7603 (t0) cc_final: 0.7056 (p0) REVERT: D 320 MET cc_start: 0.9377 (mmm) cc_final: 0.9123 (tpp) REVERT: D 368 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8238 (ttmp) REVERT: D 478 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7184 (tmmt) REVERT: D 553 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8028 (mt) REVERT: D 581 LYS cc_start: 0.7588 (tppt) cc_final: 0.7027 (mmpt) REVERT: D 672 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7945 (mmt) REVERT: D 686 LYS cc_start: 0.7926 (mttm) cc_final: 0.7701 (mmtt) REVERT: D 716 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7327 (tpm170) outliers start: 86 outliers final: 15 residues processed: 429 average time/residue: 1.3433 time to fit residues: 655.6213 Evaluate side-chains 338 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 309 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 115 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 645 GLN B 286 GLN B 643 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122276 restraints weight = 26721.400| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.34 r_work: 0.3234 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23080 Z= 0.103 Angle : 0.540 6.046 30896 Z= 0.275 Chirality : 0.037 0.136 3308 Planarity : 0.004 0.056 3716 Dihedral : 22.465 145.803 4224 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.75 % Allowed : 14.51 % Favored : 81.75 % 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: -1.61 (0.15), residues: 2552 helix: -0.26 (0.12), residues: 1604 sheet: -0.76 (0.43), residues: 112 loop : -2.62 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 692 HIS 0.006 0.001 HIS C 471 PHE 0.014 0.001 PHE B 522 TYR 0.020 0.001 TYR A 461 ARG 0.008 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 942) hydrogen bonds : angle 3.65082 ( 2778) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.38122 ( 8) covalent geometry : bond 0.00222 (23076) covalent geometry : angle 0.54044 (30888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 326 time to evaluate : 2.186 Fit side-chains REVERT: A 156 ASP cc_start: 0.7723 (t0) cc_final: 0.7228 (p0) REVERT: A 431 MET cc_start: 0.7910 (mtp) cc_final: 0.7090 (mmt) REVERT: A 478 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7064 (tmmt) REVERT: A 690 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7832 (mtm110) REVERT: B 156 ASP cc_start: 0.7692 (t0) cc_final: 0.7020 (p0) REVERT: B 159 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6546 (mmp) REVERT: B 202 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7860 (ptm160) REVERT: B 431 MET cc_start: 0.8024 (mtm) cc_final: 0.7785 (mtp) REVERT: B 478 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7255 (tmmt) REVERT: B 690 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7827 (mtm110) REVERT: B 691 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (pt) REVERT: C 286 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: C 327 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7354 (mmm-85) REVERT: C 367 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7413 (pt0) REVERT: C 478 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7145 (tmmt) REVERT: C 631 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: C 687 GLU cc_start: 0.8081 (tp30) cc_final: 0.7769 (mm-30) REVERT: C 716 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7269 (tpp-160) REVERT: D 283 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: D 368 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8195 (ttmp) REVERT: D 431 MET cc_start: 0.7847 (mtp) cc_final: 0.7076 (mmp) REVERT: D 478 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7089 (tmmt) REVERT: D 581 LYS cc_start: 0.7622 (tppt) cc_final: 0.7166 (mmpt) REVERT: D 631 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: D 686 LYS cc_start: 0.7846 (mttm) cc_final: 0.7551 (mmtt) REVERT: D 687 GLU cc_start: 0.8141 (tp30) cc_final: 0.7927 (tp30) REVERT: D 690 ARG cc_start: 0.8385 (ptp-110) cc_final: 0.7971 (mtm110) REVERT: D 716 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7319 (tpp-160) outliers start: 85 outliers final: 9 residues processed: 378 average time/residue: 1.2943 time to fit residues: 558.2572 Evaluate side-chains 317 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 631 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115205 restraints weight = 27002.345| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.33 r_work: 0.3134 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23080 Z= 0.183 Angle : 0.634 8.403 30896 Z= 0.314 Chirality : 0.041 0.156 3308 Planarity : 0.004 0.057 3716 Dihedral : 22.267 154.814 4224 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 4.50 % Allowed : 14.42 % Favored : 81.08 % 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: -0.78 (0.16), residues: 2552 helix: 0.38 (0.13), residues: 1604 sheet: -0.57 (0.43), residues: 112 loop : -2.24 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 692 HIS 0.007 0.001 HIS B 301 PHE 0.014 0.002 PHE C 316 TYR 0.026 0.002 TYR A 390 ARG 0.008 0.001 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 942) hydrogen bonds : angle 3.82576 ( 2778) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.44459 ( 8) covalent geometry : bond 0.00443 (23076) covalent geometry : angle 0.63415 (30888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 338 time to evaluate : 2.538 Fit side-chains REVERT: A 156 ASP cc_start: 0.7660 (t0) cc_final: 0.7195 (p0) REVERT: A 253 LYS cc_start: 0.8226 (ttmp) cc_final: 0.7689 (mmtt) REVERT: A 431 MET cc_start: 0.8017 (mtp) cc_final: 0.7282 (mmt) REVERT: A 478 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7017 (tmmt) REVERT: A 687 GLU cc_start: 0.8230 (tp30) cc_final: 0.8028 (tp30) REVERT: A 690 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7962 (mtm110) REVERT: A 712 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7661 (mtm110) REVERT: A 716 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.7330 (tpp-160) REVERT: B 156 ASP cc_start: 0.7528 (t0) cc_final: 0.7039 (p0) REVERT: B 159 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6677 (mmp) REVERT: B 253 LYS cc_start: 0.8237 (ttmp) cc_final: 0.7664 (mmtt) REVERT: B 368 LYS cc_start: 0.8179 (mptt) cc_final: 0.7817 (ttmp) REVERT: B 478 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7146 (tmmt) REVERT: B 690 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7959 (mtm110) REVERT: B 716 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.7326 (tpp-160) REVERT: C 133 GLU cc_start: 0.8345 (mp0) cc_final: 0.8033 (mp0) REVERT: C 156 ASP cc_start: 0.7559 (t0) cc_final: 0.7170 (p0) REVERT: C 253 LYS cc_start: 0.8184 (ttmp) cc_final: 0.7612 (mmtt) REVERT: C 327 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7467 (mmm-85) REVERT: C 367 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7337 (pt0) REVERT: C 368 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8061 (mptt) REVERT: C 478 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6994 (tmmt) REVERT: C 687 GLU cc_start: 0.8140 (tp30) cc_final: 0.7235 (tt0) REVERT: C 716 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7326 (tpm170) REVERT: C 736 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: D 202 ARG cc_start: 0.8290 (ptm160) cc_final: 0.8040 (ptm160) REVERT: D 253 LYS cc_start: 0.8090 (ttmp) cc_final: 0.7656 (mptp) REVERT: D 291 SER cc_start: 0.8907 (m) cc_final: 0.8618 (p) REVERT: D 368 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8237 (ttmp) REVERT: D 431 MET cc_start: 0.7991 (mtp) cc_final: 0.7258 (mmt) REVERT: D 478 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6956 (tmmt) REVERT: D 581 LYS cc_start: 0.7753 (tppt) cc_final: 0.7335 (mmtm) REVERT: D 686 LYS cc_start: 0.8119 (mttm) cc_final: 0.7773 (mmtt) REVERT: D 690 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8037 (mtm110) REVERT: D 691 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8715 (mt) REVERT: D 716 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7296 (tpp-160) outliers start: 102 outliers final: 32 residues processed: 398 average time/residue: 1.2844 time to fit residues: 584.1592 Evaluate side-chains 356 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 314 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 209 optimal weight: 0.0020 chunk 206 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.9748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119578 restraints weight = 26826.843| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.32 r_work: 0.3200 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23080 Z= 0.099 Angle : 0.519 6.835 30896 Z= 0.264 Chirality : 0.037 0.142 3308 Planarity : 0.004 0.057 3716 Dihedral : 21.161 145.097 4224 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.62 % Allowed : 16.18 % Favored : 80.20 % 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: -0.23 (0.17), residues: 2552 helix: 0.87 (0.13), residues: 1632 sheet: -0.28 (0.44), residues: 112 loop : -2.28 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 692 HIS 0.007 0.001 HIS B 160 PHE 0.012 0.001 PHE D 316 TYR 0.019 0.001 TYR A 461 ARG 0.011 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 942) hydrogen bonds : angle 3.48421 ( 2778) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.30805 ( 8) covalent geometry : bond 0.00222 (23076) covalent geometry : angle 0.51878 (30888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.8172 (ttmp) cc_final: 0.7647 (mmtt) REVERT: A 368 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7775 (ttmt) REVERT: A 431 MET cc_start: 0.7867 (mtp) cc_final: 0.7096 (mmt) REVERT: A 478 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6955 (tmmt) REVERT: A 690 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7885 (mtm110) REVERT: A 712 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7524 (mtt90) REVERT: A 716 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7270 (tpp-160) REVERT: B 156 ASP cc_start: 0.7374 (t0) cc_final: 0.7132 (p0) REVERT: B 253 LYS cc_start: 0.8214 (ttmp) cc_final: 0.7628 (mmtt) REVERT: B 327 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7016 (mmm-85) REVERT: B 431 MET cc_start: 0.7970 (mtm) cc_final: 0.7715 (mtp) REVERT: B 478 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7036 (tmmt) REVERT: B 641 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8117 (p0) REVERT: B 690 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7908 (mtm110) REVERT: B 716 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7295 (tpp-160) REVERT: C 156 ASP cc_start: 0.7445 (t0) cc_final: 0.7198 (p0) REVERT: C 167 THR cc_start: 0.8167 (p) cc_final: 0.7807 (t) REVERT: C 253 LYS cc_start: 0.8164 (ttmp) cc_final: 0.7605 (mmtt) REVERT: C 327 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7353 (mmm-85) REVERT: C 367 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7409 (pt0) REVERT: C 368 LYS cc_start: 0.8334 (mmmm) cc_final: 0.8018 (mptt) REVERT: C 431 MET cc_start: 0.7893 (mtp) cc_final: 0.7679 (mtp) REVERT: C 478 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6927 (tmmt) REVERT: C 687 GLU cc_start: 0.8077 (tp30) cc_final: 0.7684 (mm-30) REVERT: C 716 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7275 (tpp-160) REVERT: C 736 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: D 148 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5849 (mpt180) REVERT: D 202 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7995 (ptm160) REVERT: D 253 LYS cc_start: 0.8040 (ttmp) cc_final: 0.7639 (mmtt) REVERT: D 283 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: D 291 SER cc_start: 0.8881 (m) cc_final: 0.8612 (p) REVERT: D 368 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8206 (ttmp) REVERT: D 431 MET cc_start: 0.7914 (mtp) cc_final: 0.7159 (mmt) REVERT: D 478 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6902 (tmmt) REVERT: D 482 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6663 (pt) REVERT: D 581 LYS cc_start: 0.7694 (tppt) cc_final: 0.7335 (mmtm) REVERT: D 686 LYS cc_start: 0.8042 (mttm) cc_final: 0.7736 (mmtt) REVERT: D 690 ARG cc_start: 0.8381 (ptp-110) cc_final: 0.7950 (mtm110) REVERT: D 716 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.7315 (tpp-160) outliers start: 82 outliers final: 24 residues processed: 379 average time/residue: 1.3019 time to fit residues: 563.5548 Evaluate side-chains 334 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 681 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 24 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 139 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.167769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115681 restraints weight = 26716.801| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.31 r_work: 0.3160 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23080 Z= 0.153 Angle : 0.585 6.274 30896 Z= 0.292 Chirality : 0.040 0.151 3308 Planarity : 0.004 0.057 3716 Dihedral : 20.867 145.248 4224 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.01 % Allowed : 16.09 % Favored : 79.89 % 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: 0.10 (0.17), residues: 2552 helix: 1.12 (0.13), residues: 1608 sheet: -0.29 (0.45), residues: 112 loop : -1.99 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 692 HIS 0.006 0.001 HIS A 301 PHE 0.014 0.001 PHE C 316 TYR 0.018 0.002 TYR A 461 ARG 0.010 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 942) hydrogen bonds : angle 3.65811 ( 2778) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.35656 ( 8) covalent geometry : bond 0.00368 (23076) covalent geometry : angle 0.58465 (30888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 316 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.5302 (mpt180) REVERT: A 253 LYS cc_start: 0.8268 (ttmp) cc_final: 0.7742 (mmtt) REVERT: A 311 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: A 368 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7884 (ttmp) REVERT: A 431 MET cc_start: 0.7891 (mtp) cc_final: 0.7109 (mmt) REVERT: A 478 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6943 (tmmt) REVERT: A 642 LEU cc_start: 0.8502 (mt) cc_final: 0.8283 (mt) REVERT: A 690 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7917 (mtm110) REVERT: A 712 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7449 (mtt90) REVERT: A 716 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7291 (tpp-160) REVERT: B 148 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5268 (mpt180) REVERT: B 159 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6621 (mmp) REVERT: B 253 LYS cc_start: 0.8276 (ttmp) cc_final: 0.7664 (mmtt) REVERT: B 311 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: B 327 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7080 (mmm-85) REVERT: B 368 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7818 (ttmp) REVERT: B 478 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7034 (tmmt) REVERT: B 690 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7876 (mtm110) REVERT: B 716 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.7305 (tpm170) REVERT: C 145 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6900 (mp) REVERT: C 148 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5305 (mpt180) REVERT: C 199 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7083 (pp) REVERT: C 253 LYS cc_start: 0.8274 (ttmp) cc_final: 0.7633 (mmtt) REVERT: C 311 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7890 (ttpp) REVERT: C 327 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7374 (mmm-85) REVERT: C 367 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7333 (pt0) REVERT: C 368 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8030 (mptt) REVERT: C 478 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6877 (tmmt) REVERT: C 687 GLU cc_start: 0.8083 (tp30) cc_final: 0.7142 (tt0) REVERT: C 716 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7237 (tpm170) REVERT: C 736 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: D 145 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7128 (mt) REVERT: D 202 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7944 (ptm160) REVERT: D 253 LYS cc_start: 0.8086 (ttmp) cc_final: 0.7665 (mmtt) REVERT: D 291 SER cc_start: 0.8885 (m) cc_final: 0.8604 (p) REVERT: D 368 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8156 (ttmp) REVERT: D 431 MET cc_start: 0.7929 (mtp) cc_final: 0.7139 (mmp) REVERT: D 478 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6876 (tmmt) REVERT: D 581 LYS cc_start: 0.7590 (tppt) cc_final: 0.7212 (mmtm) REVERT: D 686 LYS cc_start: 0.7980 (mttm) cc_final: 0.7718 (mmtt) REVERT: D 690 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.7997 (mtm110) REVERT: D 691 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8613 (mt) REVERT: D 716 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7306 (tpm170) REVERT: D 741 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7404 (mp0) outliers start: 91 outliers final: 36 residues processed: 380 average time/residue: 1.3082 time to fit residues: 567.9158 Evaluate side-chains 361 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 103 optimal weight: 0.0070 chunk 247 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 200 optimal weight: 0.0470 chunk 107 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 643 ASN B 274 GLN B 643 ASN C 330 ASN C 643 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122022 restraints weight = 26826.745| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.31 r_work: 0.3235 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23080 Z= 0.086 Angle : 0.498 8.130 30896 Z= 0.254 Chirality : 0.037 0.147 3308 Planarity : 0.004 0.057 3716 Dihedral : 19.735 128.924 4224 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.69 % Allowed : 17.95 % Favored : 79.37 % 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: 0.39 (0.17), residues: 2552 helix: 1.41 (0.13), residues: 1640 sheet: -0.04 (0.45), residues: 112 loop : -2.22 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 739 HIS 0.006 0.001 HIS C 256 PHE 0.012 0.001 PHE D 316 TYR 0.012 0.001 TYR A 461 ARG 0.013 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 942) hydrogen bonds : angle 3.33084 ( 2778) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.20397 ( 8) covalent geometry : bond 0.00186 (23076) covalent geometry : angle 0.49853 (30888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5643 (OUTLIER) cc_final: 0.5427 (mpt180) REVERT: A 202 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7775 (ptm160) REVERT: A 253 LYS cc_start: 0.8224 (ttmp) cc_final: 0.7699 (mmtt) REVERT: A 431 MET cc_start: 0.7802 (mtp) cc_final: 0.7024 (mmt) REVERT: A 478 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6921 (tmmt) REVERT: A 642 LEU cc_start: 0.8434 (mt) cc_final: 0.8206 (mt) REVERT: A 690 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7793 (mtm110) REVERT: A 702 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 712 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7513 (mtt90) REVERT: A 716 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7250 (tpp-160) REVERT: B 148 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5422 (mpt180) REVERT: B 253 LYS cc_start: 0.8244 (ttmp) cc_final: 0.7654 (mmtt) REVERT: B 368 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7742 (ttmt) REVERT: B 478 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6966 (tmmt) REVERT: B 690 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7731 (mtm110) REVERT: B 702 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 716 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7190 (tpp-160) REVERT: C 145 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6909 (mp) REVERT: C 148 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.5325 (mpt180) REVERT: C 167 THR cc_start: 0.8129 (p) cc_final: 0.7794 (t) REVERT: C 199 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6969 (pp) REVERT: C 253 LYS cc_start: 0.8261 (ttmp) cc_final: 0.7647 (mmtt) REVERT: C 367 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7449 (pt0) REVERT: C 478 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6784 (tmmt) REVERT: C 641 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8047 (p0) REVERT: C 687 GLU cc_start: 0.8027 (tp30) cc_final: 0.7629 (mm-30) REVERT: C 702 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8334 (mm-30) REVERT: C 716 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7186 (tpp-160) REVERT: D 202 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7961 (ptm160) REVERT: D 253 LYS cc_start: 0.8046 (ttmp) cc_final: 0.7635 (mmtt) REVERT: D 291 SER cc_start: 0.8879 (m) cc_final: 0.8619 (p) REVERT: D 368 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8108 (ttmp) REVERT: D 431 MET cc_start: 0.7841 (mtp) cc_final: 0.7062 (mmt) REVERT: D 478 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6757 (tmmt) REVERT: D 581 LYS cc_start: 0.7575 (tppt) cc_final: 0.7244 (mmtm) REVERT: D 641 ASP cc_start: 0.8485 (p0) cc_final: 0.8281 (p0) REVERT: D 686 LYS cc_start: 0.7919 (mttm) cc_final: 0.7682 (mmtt) REVERT: D 690 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.7913 (mtm110) REVERT: D 702 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8299 (mm-30) REVERT: D 716 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7251 (tpp-160) outliers start: 61 outliers final: 19 residues processed: 369 average time/residue: 1.3167 time to fit residues: 552.3996 Evaluate side-chains 342 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 681 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 187 optimal weight: 0.4980 chunk 210 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 178 optimal weight: 0.1980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 274 GLN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118315 restraints weight = 26862.878| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.31 r_work: 0.3199 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23080 Z= 0.116 Angle : 0.539 6.871 30896 Z= 0.272 Chirality : 0.038 0.168 3308 Planarity : 0.004 0.060 3716 Dihedral : 19.560 122.957 4224 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.82 % Allowed : 17.77 % Favored : 79.41 % 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 (0.17), residues: 2552 helix: 1.55 (0.13), residues: 1612 sheet: -0.05 (0.45), residues: 112 loop : -1.96 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 710 HIS 0.005 0.001 HIS C 301 PHE 0.013 0.001 PHE A 316 TYR 0.018 0.001 TYR A 547 ARG 0.016 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 942) hydrogen bonds : angle 3.43042 ( 2778) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.29447 ( 8) covalent geometry : bond 0.00273 (23076) covalent geometry : angle 0.53939 (30888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 310 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.5400 (mpt180) REVERT: A 253 LYS cc_start: 0.8274 (ttmp) cc_final: 0.7728 (mmtt) REVERT: A 368 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7863 (ttmt) REVERT: A 431 MET cc_start: 0.7827 (mtp) cc_final: 0.7043 (mmp) REVERT: A 478 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6908 (tmmt) REVERT: A 642 LEU cc_start: 0.8488 (mt) cc_final: 0.8265 (mt) REVERT: A 690 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7843 (mtm110) REVERT: A 702 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 712 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7490 (mtt90) REVERT: A 716 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7273 (tpp-160) REVERT: B 148 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5444 (mpt180) REVERT: B 159 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6686 (mmp) REVERT: B 253 LYS cc_start: 0.8276 (ttmp) cc_final: 0.7673 (mmtt) REVERT: B 478 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6940 (tmmt) REVERT: B 690 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7789 (mtm110) REVERT: B 702 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8325 (mm-30) REVERT: B 716 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7259 (tpp-160) REVERT: B 741 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 145 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6875 (mp) REVERT: C 148 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5351 (mpt180) REVERT: C 167 THR cc_start: 0.8191 (p) cc_final: 0.7859 (t) REVERT: C 199 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7057 (pp) REVERT: C 253 LYS cc_start: 0.8299 (ttmp) cc_final: 0.7651 (mmtt) REVERT: C 367 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7437 (pt0) REVERT: C 478 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6852 (tmmt) REVERT: C 641 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 702 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8348 (mm-30) REVERT: C 716 ARG cc_start: 0.8261 (ttp-170) cc_final: 0.7232 (tpp-160) REVERT: C 736 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7267 (pt0) REVERT: D 202 ARG cc_start: 0.8231 (ptm160) cc_final: 0.7931 (ptm160) REVERT: D 253 LYS cc_start: 0.8066 (ttmp) cc_final: 0.7668 (mmtt) REVERT: D 291 SER cc_start: 0.8881 (m) cc_final: 0.8619 (p) REVERT: D 368 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8160 (ttmt) REVERT: D 431 MET cc_start: 0.7904 (mtp) cc_final: 0.7110 (mmp) REVERT: D 478 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6787 (tmmt) REVERT: D 581 LYS cc_start: 0.7588 (tppt) cc_final: 0.7221 (mmtm) REVERT: D 641 ASP cc_start: 0.8482 (p0) cc_final: 0.8273 (p0) REVERT: D 686 LYS cc_start: 0.7995 (mttm) cc_final: 0.7740 (mmtt) REVERT: D 690 ARG cc_start: 0.8465 (ptp-110) cc_final: 0.8009 (mtm110) REVERT: D 702 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8349 (mm-30) REVERT: D 716 ARG cc_start: 0.8289 (ttp-170) cc_final: 0.7274 (tpp-160) outliers start: 64 outliers final: 24 residues processed: 355 average time/residue: 1.3534 time to fit residues: 549.7732 Evaluate side-chains 340 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 138 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116479 restraints weight = 26675.932| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.35 r_work: 0.3179 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23080 Z= 0.148 Angle : 0.587 8.065 30896 Z= 0.294 Chirality : 0.040 0.181 3308 Planarity : 0.004 0.070 3716 Dihedral : 19.549 117.994 4224 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.82 % Allowed : 17.95 % Favored : 79.23 % 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: 0.47 (0.17), residues: 2552 helix: 1.43 (0.13), residues: 1624 sheet: -0.09 (0.46), residues: 112 loop : -1.99 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 710 HIS 0.009 0.001 HIS B 160 PHE 0.013 0.001 PHE B 316 TYR 0.016 0.002 TYR A 461 ARG 0.019 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 942) hydrogen bonds : angle 3.56834 ( 2778) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.35249 ( 8) covalent geometry : bond 0.00360 (23076) covalent geometry : angle 0.58724 (30888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5656 (mpt180) REVERT: A 253 LYS cc_start: 0.8269 (ttmp) cc_final: 0.7683 (mmtt) REVERT: A 368 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7925 (ttmp) REVERT: A 431 MET cc_start: 0.7876 (mtp) cc_final: 0.7162 (mmt) REVERT: A 478 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6824 (tmmt) REVERT: A 488 MET cc_start: 0.8185 (mmp) cc_final: 0.7904 (tpt) REVERT: A 642 LEU cc_start: 0.8448 (mt) cc_final: 0.8209 (mt) REVERT: A 690 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7772 (mtm110) REVERT: A 712 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7396 (mtt90) REVERT: A 716 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7280 (tpp-160) REVERT: B 148 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5582 (mpt180) REVERT: B 159 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6698 (mmp) REVERT: B 253 LYS cc_start: 0.8334 (ttmp) cc_final: 0.7698 (mmtt) REVERT: B 368 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7794 (ttmt) REVERT: B 478 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6877 (tmmt) REVERT: B 581 LYS cc_start: 0.8476 (tmtt) cc_final: 0.6834 (mmtm) REVERT: B 690 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7828 (mtm110) REVERT: B 716 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7252 (tpp-160) REVERT: B 741 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: C 145 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6860 (mp) REVERT: C 148 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.5474 (mpt180) REVERT: C 167 THR cc_start: 0.8272 (p) cc_final: 0.7921 (t) REVERT: C 199 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7034 (pp) REVERT: C 253 LYS cc_start: 0.8365 (ttmp) cc_final: 0.7719 (mmtt) REVERT: C 367 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7340 (pt0) REVERT: C 478 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6737 (tmmt) REVERT: C 488 MET cc_start: 0.8144 (mmp) cc_final: 0.7882 (tpt) REVERT: C 687 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7319 (tm-30) REVERT: C 716 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7237 (tpp-160) REVERT: C 736 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: D 253 LYS cc_start: 0.8169 (ttmp) cc_final: 0.7742 (mptp) REVERT: D 291 SER cc_start: 0.8876 (m) cc_final: 0.8616 (p) REVERT: D 368 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8174 (ttmt) REVERT: D 431 MET cc_start: 0.7889 (mtp) cc_final: 0.7085 (mmp) REVERT: D 478 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6795 (tmmt) REVERT: D 488 MET cc_start: 0.8103 (mmp) cc_final: 0.7830 (tpt) REVERT: D 581 LYS cc_start: 0.7522 (tppt) cc_final: 0.7154 (mmtm) REVERT: D 686 LYS cc_start: 0.8092 (mttm) cc_final: 0.7825 (mttm) REVERT: D 690 ARG cc_start: 0.8488 (ptp-110) cc_final: 0.8028 (mtm110) REVERT: D 702 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 716 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7259 (tpp-160) outliers start: 64 outliers final: 28 residues processed: 349 average time/residue: 1.3602 time to fit residues: 540.0744 Evaluate side-chains 339 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 237 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.0050 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN B 160 HIS B 643 ASN C 330 ASN C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122054 restraints weight = 26745.594| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.34 r_work: 0.3257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23080 Z= 0.091 Angle : 0.526 9.928 30896 Z= 0.266 Chirality : 0.037 0.148 3308 Planarity : 0.004 0.082 3716 Dihedral : 18.672 109.890 4224 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.76 % Allowed : 19.18 % Favored : 79.06 % 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: 0.78 (0.17), residues: 2552 helix: 1.69 (0.13), residues: 1624 sheet: 0.07 (0.47), residues: 112 loop : -1.90 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 739 HIS 0.008 0.001 HIS B 160 PHE 0.012 0.001 PHE B 316 TYR 0.017 0.001 TYR A 547 ARG 0.020 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.02665 ( 942) hydrogen bonds : angle 3.33550 ( 2778) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.23701 ( 8) covalent geometry : bond 0.00202 (23076) covalent geometry : angle 0.52638 (30888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5649 (mpt180) REVERT: A 253 LYS cc_start: 0.8184 (ttmp) cc_final: 0.7686 (mmtt) REVERT: A 431 MET cc_start: 0.7909 (mtp) cc_final: 0.7107 (mmp) REVERT: A 478 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6738 (ttpt) REVERT: A 642 LEU cc_start: 0.8373 (mt) cc_final: 0.8153 (mt) REVERT: A 690 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7783 (mtm110) REVERT: A 702 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 712 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7466 (mtt90) REVERT: A 716 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7250 (tpp-160) REVERT: B 148 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.5589 (mpt180) REVERT: B 253 LYS cc_start: 0.8271 (ttmp) cc_final: 0.7679 (mmtt) REVERT: B 478 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6885 (tmmt) REVERT: B 488 MET cc_start: 0.8222 (mmp) cc_final: 0.7886 (tpt) REVERT: B 581 LYS cc_start: 0.8464 (tmtt) cc_final: 0.6836 (mmtm) REVERT: B 690 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7769 (mtm110) REVERT: B 702 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 716 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7224 (tpp-160) REVERT: B 741 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: C 145 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6844 (mp) REVERT: C 148 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.5515 (mpt180) REVERT: C 167 THR cc_start: 0.8175 (p) cc_final: 0.7893 (t) REVERT: C 199 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6985 (pp) REVERT: C 253 LYS cc_start: 0.8279 (ttmp) cc_final: 0.7667 (mmtt) REVERT: C 367 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7428 (pt0) REVERT: C 478 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6860 (tmmt) REVERT: C 488 MET cc_start: 0.8218 (mmp) cc_final: 0.7921 (tpt) REVERT: C 687 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7819 (tp30) REVERT: C 690 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7616 (mtm110) REVERT: C 702 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8277 (mm-30) REVERT: C 716 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7235 (tpm170) REVERT: D 253 LYS cc_start: 0.8065 (ttmp) cc_final: 0.7657 (mptp) REVERT: D 291 SER cc_start: 0.8873 (m) cc_final: 0.8636 (p) REVERT: D 368 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8141 (ttmt) REVERT: D 431 MET cc_start: 0.7805 (mtp) cc_final: 0.7025 (mmt) REVERT: D 478 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6833 (tmmt) REVERT: D 488 MET cc_start: 0.8113 (mmp) cc_final: 0.7813 (tpt) REVERT: D 581 LYS cc_start: 0.7484 (tppt) cc_final: 0.7142 (mmtm) REVERT: D 686 LYS cc_start: 0.7950 (mttm) cc_final: 0.7720 (mttm) REVERT: D 690 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7965 (mtm110) REVERT: D 702 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 716 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7239 (tpm170) outliers start: 40 outliers final: 22 residues processed: 341 average time/residue: 1.3107 time to fit residues: 509.5756 Evaluate side-chains 343 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 226 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 160 HIS B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116271 restraints weight = 26198.731| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.36 r_work: 0.3151 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23080 Z= 0.129 Angle : 0.571 9.809 30896 Z= 0.287 Chirality : 0.039 0.161 3308 Planarity : 0.004 0.077 3716 Dihedral : 18.752 107.547 4224 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.54 % Allowed : 19.58 % Favored : 78.88 % 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 (0.17), residues: 2552 helix: 1.63 (0.13), residues: 1624 sheet: 0.05 (0.48), residues: 112 loop : -1.93 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 710 HIS 0.010 0.001 HIS B 160 PHE 0.012 0.001 PHE B 316 TYR 0.016 0.002 TYR A 540 ARG 0.019 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 942) hydrogen bonds : angle 3.46077 ( 2778) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.31998 ( 8) covalent geometry : bond 0.00310 (23076) covalent geometry : angle 0.57135 (30888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19652.29 seconds wall clock time: 338 minutes 9.68 seconds (20289.68 seconds total)