Starting phenix.real_space_refine on Thu Jun 19 08:58:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6o_42998/06_2025/8v6o_42998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6o_42998/06_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_42998/06_2025/8v6o_42998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6o_42998/06_2025/8v6o_42998.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6o_42998/06_2025/8v6o_42998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6o_42998/06_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-5710/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: 13.43, per 1000 atoms: 0.59 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: 6.31 Conformation dependent library (CDL) restraints added in 2.6 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: 2.14 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: 6.90 Time building geometry restraints manager: 7.21 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: 1.330 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: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 49.430 Find NCS groups from input model: 1.280 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.650 ------------------------------------------------------------------------------- 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 : 2.250 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: 1.4439 time to fit residues: 955.3410 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 : 1.936 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.172773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119907 restraints weight = 26622.931| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.33 r_work: 0.3216 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- 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 : 2.254 Fit side-chains REVERT: A 220 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8283 (m-40) REVERT: A 431 MET cc_start: 0.8041 (mtp) cc_final: 0.7188 (mmt) REVERT: A 478 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7151 (tmmt) REVERT: A 631 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 690 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7761 (mtm110) REVERT: A 712 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7529 (mtt90) REVERT: B 159 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6543 (mmp) REVERT: B 202 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7730 (ptm160) REVERT: B 478 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7237 (tmmt) REVERT: B 631 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 690 ARG cc_start: 0.8380 (mtt90) cc_final: 0.7799 (mtm110) REVERT: B 716 ARG cc_start: 0.8289 (ttp-170) cc_final: 0.7296 (tpp-160) REVERT: C 327 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7455 (mmm-85) REVERT: C 367 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7356 (pt0) REVERT: C 478 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7182 (tmmt) REVERT: C 631 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: C 712 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7786 (mtm110) REVERT: C 716 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.7351 (tpm170) REVERT: D 156 ASP cc_start: 0.7603 (t0) cc_final: 0.7055 (p0) REVERT: D 320 MET cc_start: 0.9377 (mmm) cc_final: 0.9123 (tpp) REVERT: D 368 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8239 (ttmp) REVERT: D 478 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7185 (tmmt) REVERT: D 553 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (mt) REVERT: D 581 LYS cc_start: 0.7590 (tppt) cc_final: 0.7027 (mmpt) REVERT: D 672 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7942 (mmt) REVERT: D 686 LYS cc_start: 0.7929 (mttm) cc_final: 0.7703 (mmtt) REVERT: D 716 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7327 (tpm170) outliers start: 86 outliers final: 15 residues processed: 429 average time/residue: 1.4346 time to fit residues: 699.8395 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 : 2.432 ------------------------------------------------------------------------------- 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: 0.9980 chunk 235 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN 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 = 0.3988 r_free = 0.3988 target = 0.174286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122645 restraints weight = 26713.840| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.34 r_work: 0.3257 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 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 = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23080 Z= 0.100 Angle : 0.537 6.009 30896 Z= 0.274 Chirality : 0.037 0.135 3308 Planarity : 0.004 0.056 3716 Dihedral : 22.459 145.644 4224 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.75 % Allowed : 14.46 % Favored : 81.79 % 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: -1.59 (0.15), residues: 2552 helix: -0.25 (0.12), residues: 1604 sheet: -0.74 (0.43), residues: 112 loop : -2.62 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 692 HIS 0.006 0.001 HIS D 471 PHE 0.014 0.001 PHE B 522 TYR 0.021 0.001 TYR A 461 ARG 0.008 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 942) hydrogen bonds : angle 3.64293 ( 2778) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.40068 ( 8) covalent geometry : bond 0.00216 (23076) covalent geometry : angle 0.53697 (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 412 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 3.089 Fit side-chains REVERT: A 156 ASP cc_start: 0.7736 (t0) cc_final: 0.7222 (p0) REVERT: A 431 MET cc_start: 0.7895 (mtp) cc_final: 0.7085 (mmt) REVERT: A 478 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7062 (tmmt) REVERT: A 690 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7817 (mtm110) REVERT: A 691 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8184 (pt) REVERT: B 156 ASP cc_start: 0.7692 (t0) cc_final: 0.7019 (p0) REVERT: B 159 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6540 (mmp) REVERT: B 202 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7864 (ptm160) REVERT: B 431 MET cc_start: 0.8006 (mtm) cc_final: 0.7785 (mtp) REVERT: B 478 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7248 (tmmt) REVERT: B 687 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7988 (mm-30) REVERT: B 690 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7754 (mtm110) REVERT: B 691 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8180 (pt) REVERT: C 286 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: C 327 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7360 (mmm-85) REVERT: C 367 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7418 (pt0) REVERT: C 478 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7161 (tmmt) REVERT: C 631 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: C 687 GLU cc_start: 0.8074 (tp30) cc_final: 0.7770 (mm-30) REVERT: C 716 ARG cc_start: 0.8257 (ttp-170) cc_final: 0.7277 (tpp-160) REVERT: D 283 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: D 368 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8194 (ttmp) REVERT: D 431 MET cc_start: 0.7839 (mtp) cc_final: 0.7058 (mmp) REVERT: D 478 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7089 (tmmt) REVERT: D 581 LYS cc_start: 0.7603 (tppt) cc_final: 0.7151 (mmpt) REVERT: D 631 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: D 686 LYS cc_start: 0.7864 (mttm) cc_final: 0.7546 (mmtt) REVERT: D 687 GLU cc_start: 0.8133 (tp30) cc_final: 0.7931 (tp30) REVERT: D 690 ARG cc_start: 0.8412 (ptp-110) cc_final: 0.7970 (mtm110) REVERT: D 716 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7322 (tpp-160) outliers start: 85 outliers final: 10 residues processed: 379 average time/residue: 1.4039 time to fit residues: 606.7150 Evaluate side-chains 321 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 299 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 691 ILE 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 356 ILE Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 541 LEU 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: 5.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** D 279 GLN D 330 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 = 0.3930 r_free = 0.3930 target = 0.168705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116139 restraints weight = 27018.768| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.33 r_work: 0.3147 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4364 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= 0.160 Angle : 0.608 8.045 30896 Z= 0.303 Chirality : 0.040 0.152 3308 Planarity : 0.004 0.056 3716 Dihedral : 22.086 153.575 4224 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.19 % Allowed : 14.59 % Favored : 81.22 % 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: -0.83 (0.16), residues: 2552 helix: 0.36 (0.13), residues: 1628 sheet: -0.50 (0.43), residues: 112 loop : -2.41 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 692 HIS 0.006 0.001 HIS C 301 PHE 0.014 0.001 PHE D 316 TYR 0.024 0.002 TYR A 390 ARG 0.007 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 942) hydrogen bonds : angle 3.76392 ( 2778) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.42434 ( 8) covalent geometry : bond 0.00382 (23076) covalent geometry : angle 0.60817 (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 422 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 327 time to evaluate : 2.414 Fit side-chains REVERT: A 156 ASP cc_start: 0.7665 (t0) cc_final: 0.7190 (p0) REVERT: A 253 LYS cc_start: 0.8163 (ttmp) cc_final: 0.7648 (mmtt) REVERT: A 431 MET cc_start: 0.8010 (mtp) cc_final: 0.7255 (mmt) REVERT: A 478 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7076 (tmmt) REVERT: A 690 ARG cc_start: 0.8440 (mtt90) cc_final: 0.7962 (mtm110) REVERT: A 712 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7704 (mtm110) REVERT: A 716 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7308 (tpp-160) REVERT: B 156 ASP cc_start: 0.7509 (t0) cc_final: 0.7010 (p0) REVERT: B 159 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6734 (mmp) REVERT: B 253 LYS cc_start: 0.8209 (ttmp) cc_final: 0.7661 (mmtt) REVERT: B 368 LYS cc_start: 0.8171 (mptt) cc_final: 0.7816 (ttmp) REVERT: B 478 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7111 (tmmt) REVERT: B 690 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7986 (mtm110) REVERT: B 691 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (pt) REVERT: B 716 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7338 (tpp-160) REVERT: C 133 GLU cc_start: 0.8382 (mp0) cc_final: 0.8088 (mp0) REVERT: C 156 ASP cc_start: 0.7563 (t0) cc_final: 0.7176 (p0) REVERT: C 327 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7451 (mmm-85) REVERT: C 367 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7364 (pt0) REVERT: C 368 LYS cc_start: 0.8323 (mmmm) cc_final: 0.8006 (mptt) REVERT: C 478 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7002 (tmmt) REVERT: C 687 GLU cc_start: 0.8139 (tp30) cc_final: 0.7698 (mm-30) REVERT: C 716 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.7356 (tpm170) REVERT: C 736 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: D 202 ARG cc_start: 0.8281 (ptm160) cc_final: 0.8037 (ptm160) REVERT: D 253 LYS cc_start: 0.8049 (ttmp) cc_final: 0.7636 (mptp) REVERT: D 291 SER cc_start: 0.8905 (m) cc_final: 0.8620 (p) REVERT: D 368 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8217 (ttmp) REVERT: D 431 MET cc_start: 0.8021 (mtp) cc_final: 0.7284 (mmt) REVERT: D 478 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6956 (tmmt) REVERT: D 581 LYS cc_start: 0.7772 (tppt) cc_final: 0.7368 (mmtm) REVERT: D 686 LYS cc_start: 0.8104 (mttm) cc_final: 0.7773 (mmtt) REVERT: D 690 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8038 (mtm110) REVERT: D 691 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 716 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7323 (tpp-160) outliers start: 95 outliers final: 26 residues processed: 384 average time/residue: 1.3481 time to fit residues: 590.1362 Evaluate side-chains 348 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 323 MET 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 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 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 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 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 478 LYS Chi-restraints excluded: chain D residue 536 SER 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: 7.9990 chunk 84 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.169140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117100 restraints weight = 26834.526| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.32 r_work: 0.3167 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- 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: 33 | |-----------------------------------------------------------------------------| |-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: 34 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23080 Z= 0.134 Angle : 0.555 6.658 30896 Z= 0.280 Chirality : 0.039 0.146 3308 Planarity : 0.004 0.057 3716 Dihedral : 21.268 147.079 4224 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.50 % Allowed : 15.26 % Favored : 80.25 % 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: -0.32 (0.17), residues: 2552 helix: 0.80 (0.13), residues: 1644 sheet: -0.38 (0.44), residues: 112 loop : -2.35 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.006 0.001 HIS B 160 PHE 0.014 0.001 PHE D 316 TYR 0.022 0.002 TYR A 461 ARG 0.010 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 942) hydrogen bonds : angle 3.58927 ( 2778) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.37559 ( 8) covalent geometry : bond 0.00319 (23076) covalent geometry : angle 0.55510 (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 431 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 329 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6926 (mp) REVERT: A 148 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.5278 (mpt180) REVERT: A 253 LYS cc_start: 0.8236 (ttmp) cc_final: 0.7637 (mmtt) REVERT: A 368 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7838 (ttmt) REVERT: A 431 MET cc_start: 0.7892 (mtp) cc_final: 0.7078 (mmt) REVERT: A 478 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6998 (tmmt) REVERT: A 690 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7872 (mtm110) REVERT: A 712 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7529 (mtt90) REVERT: A 716 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7253 (tpp-160) REVERT: B 199 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6890 (pp) REVERT: B 253 LYS cc_start: 0.8243 (ttmp) cc_final: 0.7612 (mmtt) REVERT: B 327 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7023 (mmm-85) REVERT: B 368 LYS cc_start: 0.8169 (mptt) cc_final: 0.7801 (ttmp) REVERT: B 431 MET cc_start: 0.7988 (mtm) cc_final: 0.7751 (mtp) REVERT: B 478 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7038 (tmmt) REVERT: B 631 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: B 690 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7859 (mtm110) REVERT: B 716 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.7307 (tpm170) REVERT: C 253 LYS cc_start: 0.8260 (ttmp) cc_final: 0.7608 (mmtt) REVERT: C 327 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7354 (mmm-85) REVERT: C 367 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7355 (pt0) REVERT: C 368 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8043 (mptt) REVERT: C 431 MET cc_start: 0.7917 (mtp) cc_final: 0.7678 (mtp) REVERT: C 478 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6917 (tmmt) REVERT: C 631 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: C 687 GLU cc_start: 0.8062 (tp30) cc_final: 0.7708 (mm-30) REVERT: C 716 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7236 (tpp-160) REVERT: C 736 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: D 202 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7942 (ptm160) REVERT: D 253 LYS cc_start: 0.8102 (ttmp) cc_final: 0.7662 (mmtt) REVERT: D 283 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: D 291 SER cc_start: 0.8894 (m) cc_final: 0.8608 (p) REVERT: D 368 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8175 (ttmp) REVERT: D 431 MET cc_start: 0.7919 (mtp) cc_final: 0.7127 (mmt) REVERT: D 478 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6885 (tmmt) REVERT: D 581 LYS cc_start: 0.7698 (tppt) cc_final: 0.7301 (mmtm) REVERT: D 686 LYS cc_start: 0.7992 (mttm) cc_final: 0.7697 (mmtt) REVERT: D 690 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.7965 (mtm110) REVERT: D 691 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8540 (mt) REVERT: D 716 ARG cc_start: 0.8330 (ttp-170) cc_final: 0.7361 (tpm170) outliers start: 102 outliers final: 29 residues processed: 403 average time/residue: 1.3431 time to fit residues: 618.3578 Evaluate side-chains 346 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 ASP 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 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 199 ILE Chi-restraints excluded: chain B residue 229 ASP 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 631 GLU 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 323 MET 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 631 GLU Chi-restraints excluded: chain C residue 736 GLU 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 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 691 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 24 optimal weight: 0.0570 chunk 193 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 99 optimal weight: 0.0770 chunk 194 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 160 HIS B 643 ASN C 160 HIS C 330 ASN C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120462 restraints weight = 26752.748| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.31 r_work: 0.3210 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23080 Z= 0.092 Angle : 0.506 7.847 30896 Z= 0.257 Chirality : 0.037 0.138 3308 Planarity : 0.004 0.056 3716 Dihedral : 20.260 142.395 4224 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.69 % Allowed : 17.59 % Favored : 79.72 % 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: 0.14 (0.17), residues: 2552 helix: 1.20 (0.13), residues: 1648 sheet: -0.19 (0.44), residues: 112 loop : -2.29 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 692 HIS 0.007 0.001 HIS B 160 PHE 0.012 0.001 PHE D 316 TYR 0.016 0.001 TYR B 461 ARG 0.009 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.02800 ( 942) hydrogen bonds : angle 3.39805 ( 2778) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.23765 ( 8) covalent geometry : bond 0.00202 (23076) covalent geometry : angle 0.50625 (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 387 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 326 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ARG cc_start: 0.8027 (ptm160) cc_final: 0.7763 (ptm160) REVERT: A 253 LYS cc_start: 0.8179 (ttmp) cc_final: 0.7634 (mmtt) REVERT: A 431 MET cc_start: 0.7822 (mtp) cc_final: 0.7054 (mmt) REVERT: A 478 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.6937 (ttpt) REVERT: A 687 GLU cc_start: 0.8130 (tp30) cc_final: 0.7912 (tp30) REVERT: A 690 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7723 (mtm110) REVERT: A 702 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 712 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7457 (mtt90) REVERT: A 716 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7221 (tpp-160) REVERT: B 148 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.5310 (mpt180) REVERT: B 253 LYS cc_start: 0.8229 (ttmp) cc_final: 0.7641 (mmtt) REVERT: B 327 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6969 (mmm-85) REVERT: B 368 LYS cc_start: 0.8164 (mptt) cc_final: 0.7786 (ttmp) REVERT: B 431 MET cc_start: 0.7905 (mtm) cc_final: 0.7684 (mtp) REVERT: B 478 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7055 (tmmt) REVERT: B 690 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7831 (mtm110) REVERT: B 702 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 716 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7243 (tpp-160) REVERT: C 148 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.5253 (mpt180) REVERT: C 167 THR cc_start: 0.8123 (p) cc_final: 0.7790 (t) REVERT: C 253 LYS cc_start: 0.8263 (ttmp) cc_final: 0.7629 (mmtt) REVERT: C 327 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7362 (mmm-85) REVERT: C 367 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7428 (pt0) REVERT: C 431 MET cc_start: 0.7830 (mtp) cc_final: 0.7621 (mtp) REVERT: C 478 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6935 (tmmt) REVERT: C 687 GLU cc_start: 0.8035 (tp30) cc_final: 0.7606 (mm-30) REVERT: C 702 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8283 (mm-30) REVERT: C 716 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7246 (tpp-160) REVERT: C 736 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7222 (pt0) REVERT: D 202 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7957 (ptm160) REVERT: D 253 LYS cc_start: 0.8087 (ttmp) cc_final: 0.7661 (mmtt) REVERT: D 291 SER cc_start: 0.8894 (m) cc_final: 0.8619 (p) REVERT: D 368 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8096 (ttmp) REVERT: D 431 MET cc_start: 0.7868 (mtp) cc_final: 0.7078 (mmt) REVERT: D 478 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6893 (tmmt) REVERT: D 581 LYS cc_start: 0.7590 (tppt) cc_final: 0.7235 (mmtm) REVERT: D 686 LYS cc_start: 0.7920 (mttm) cc_final: 0.7653 (mmtt) REVERT: D 690 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.7937 (mtm110) REVERT: D 702 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8332 (mm-30) REVERT: D 716 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7285 (tpp-160) outliers start: 61 outliers final: 19 residues processed: 366 average time/residue: 1.4092 time to fit residues: 585.0093 Evaluate side-chains 337 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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 327 ARG 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 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 681 VAL Chi-restraints excluded: chain C residue 148 ARG 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 732 LEU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 103 optimal weight: 0.0980 chunk 247 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.171005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119243 restraints weight = 26842.400| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.31 r_work: 0.3190 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23080 Z= 0.103 Angle : 0.522 8.289 30896 Z= 0.265 Chirality : 0.038 0.154 3308 Planarity : 0.004 0.056 3716 Dihedral : 19.716 136.059 4224 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.73 % Allowed : 17.55 % Favored : 79.72 % 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: 0.38 (0.17), residues: 2552 helix: 1.39 (0.13), residues: 1640 sheet: -0.10 (0.45), residues: 112 loop : -2.18 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 521 HIS 0.008 0.001 HIS B 160 PHE 0.013 0.001 PHE A 316 TYR 0.015 0.001 TYR A 461 ARG 0.010 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 942) hydrogen bonds : angle 3.40570 ( 2778) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.26684 ( 8) covalent geometry : bond 0.00237 (23076) covalent geometry : angle 0.52253 (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 375 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6887 (mp) REVERT: A 188 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7496 (mmm-85) REVERT: A 253 LYS cc_start: 0.8246 (ttmp) cc_final: 0.7653 (mmtt) REVERT: A 431 MET cc_start: 0.7844 (mtp) cc_final: 0.7074 (mmt) REVERT: A 478 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6913 (tmmt) REVERT: A 690 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7850 (mtm110) REVERT: A 702 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 712 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7497 (mtt90) REVERT: A 716 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7238 (tpp-160) REVERT: B 148 ARG cc_start: 0.5660 (OUTLIER) cc_final: 0.5412 (mpt180) REVERT: B 253 LYS cc_start: 0.8279 (ttmp) cc_final: 0.7671 (mmtt) REVERT: B 368 LYS cc_start: 0.8165 (mptt) cc_final: 0.7806 (ttmp) REVERT: B 478 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6977 (tmmt) REVERT: B 581 LYS cc_start: 0.8530 (tmtt) cc_final: 0.6931 (mmtm) REVERT: B 690 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7814 (mtm110) REVERT: B 716 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7257 (tpm170) REVERT: C 148 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.5282 (mpt180) REVERT: C 167 THR cc_start: 0.8180 (p) cc_final: 0.7829 (t) REVERT: C 202 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7831 (ptm160) REVERT: C 253 LYS cc_start: 0.8298 (ttmp) cc_final: 0.7648 (mmtt) REVERT: C 367 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7458 (pt0) REVERT: C 478 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6795 (tmmt) REVERT: C 687 GLU cc_start: 0.8062 (tp30) cc_final: 0.7610 (mm-30) REVERT: C 702 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 716 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7251 (tpp-160) REVERT: C 736 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: D 202 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7954 (ptm160) REVERT: D 253 LYS cc_start: 0.8051 (ttmp) cc_final: 0.7661 (mmtt) REVERT: D 291 SER cc_start: 0.8896 (m) cc_final: 0.8627 (p) REVERT: D 318 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8291 (ptpt) REVERT: D 368 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8094 (ttmp) REVERT: D 431 MET cc_start: 0.7917 (mtp) cc_final: 0.7122 (mmt) REVERT: D 478 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6730 (tmmt) REVERT: D 581 LYS cc_start: 0.7612 (tppt) cc_final: 0.7244 (mmtm) REVERT: D 686 LYS cc_start: 0.7979 (mttm) cc_final: 0.7710 (mmtt) REVERT: D 690 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.7976 (mtm110) REVERT: D 702 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8364 (mm-30) REVERT: D 716 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.7294 (tpp-160) outliers start: 62 outliers final: 25 residues processed: 351 average time/residue: 1.3826 time to fit residues: 550.0461 Evaluate side-chains 337 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU 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 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 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 C residue 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS 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 732 LEU Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 318 LYS 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 536 SER Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 187 optimal weight: 0.0670 chunk 210 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 178 optimal weight: 0.7980 overall best weight: 2.9724 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114913 restraints weight = 26705.749| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.36 r_work: 0.3169 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5124 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= 0.179 Angle : 0.624 8.248 30896 Z= 0.309 Chirality : 0.041 0.177 3308 Planarity : 0.004 0.056 3716 Dihedral : 20.070 126.848 4224 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.26 % Allowed : 17.15 % Favored : 79.59 % 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: 0.29 (0.17), residues: 2552 helix: 1.27 (0.13), residues: 1632 sheet: -0.17 (0.46), residues: 112 loop : -2.05 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 710 HIS 0.009 0.001 HIS B 160 PHE 0.013 0.001 PHE A 316 TYR 0.018 0.002 TYR A 461 ARG 0.015 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 942) hydrogen bonds : angle 3.69632 ( 2778) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.38000 ( 8) covalent geometry : bond 0.00435 (23076) covalent geometry : angle 0.62358 (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 379 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 305 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.8249 (ttmp) cc_final: 0.7662 (mmtt) REVERT: A 311 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7857 (ttpp) REVERT: A 368 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7969 (ttmp) REVERT: A 431 MET cc_start: 0.7887 (mtp) cc_final: 0.7158 (mmt) REVERT: A 478 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6829 (tmmt) REVERT: A 690 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7865 (mtm110) REVERT: A 712 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7443 (mtt90) REVERT: A 716 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7305 (tpp-160) REVERT: A 741 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: B 148 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5483 (mpt180) REVERT: B 253 LYS cc_start: 0.8336 (ttmp) cc_final: 0.7688 (mmtt) REVERT: B 311 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7889 (ttpp) REVERT: B 431 MET cc_start: 0.7934 (mtp) cc_final: 0.7705 (mtp) REVERT: B 478 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6920 (tmmt) REVERT: B 488 MET cc_start: 0.8173 (mmp) cc_final: 0.7926 (tpt) REVERT: B 690 ARG cc_start: 0.8239 (mtt90) cc_final: 0.7845 (mtm110) REVERT: B 702 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 716 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.7246 (tpp-160) REVERT: C 148 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.5364 (mpt180) REVERT: C 253 LYS cc_start: 0.8356 (ttmp) cc_final: 0.7710 (mmtt) REVERT: C 367 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7331 (pt0) REVERT: C 478 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6696 (tmmt) REVERT: C 488 MET cc_start: 0.8223 (mmp) cc_final: 0.7991 (tpt) REVERT: C 687 GLU cc_start: 0.8097 (tp30) cc_final: 0.7083 (tt0) REVERT: C 716 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7228 (tpp-160) REVERT: C 736 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: D 253 LYS cc_start: 0.8187 (ttmp) cc_final: 0.7784 (mptp) REVERT: D 291 SER cc_start: 0.8887 (m) cc_final: 0.8618 (p) REVERT: D 368 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8192 (ttmt) REVERT: D 431 MET cc_start: 0.7896 (mtp) cc_final: 0.7126 (mmt) REVERT: D 478 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6755 (tmmt) REVERT: D 488 MET cc_start: 0.8190 (mmp) cc_final: 0.7973 (tpt) REVERT: D 581 LYS cc_start: 0.7538 (tppt) cc_final: 0.7170 (mmtm) REVERT: D 686 LYS cc_start: 0.8037 (mttm) cc_final: 0.7777 (mmtt) REVERT: D 690 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8032 (mtm110) REVERT: D 691 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8687 (mt) REVERT: D 716 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.7284 (tpm170) REVERT: D 741 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7353 (mp0) outliers start: 74 outliers final: 32 residues processed: 358 average time/residue: 1.5142 time to fit residues: 618.0448 Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain A residue 318 LYS 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 740 THR Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 311 LYS 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 148 ARG Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS 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 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 536 SER Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 138 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.172064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120226 restraints weight = 26689.258| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.34 r_work: 0.3236 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5185 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= 0.096 Angle : 0.523 7.712 30896 Z= 0.265 Chirality : 0.038 0.157 3308 Planarity : 0.004 0.077 3716 Dihedral : 19.093 116.013 4224 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.90 % Allowed : 19.00 % Favored : 79.10 % 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: 0.66 (0.17), residues: 2552 helix: 1.60 (0.13), residues: 1624 sheet: -0.04 (0.47), residues: 112 loop : -1.94 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 710 HIS 0.008 0.001 HIS B 160 PHE 0.012 0.001 PHE A 316 TYR 0.015 0.001 TYR A 461 ARG 0.019 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.02817 ( 942) hydrogen bonds : angle 3.38987 ( 2778) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.24836 ( 8) covalent geometry : bond 0.00215 (23076) covalent geometry : angle 0.52295 (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 360 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.8258 (ttmp) cc_final: 0.7667 (mmtt) REVERT: A 368 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7884 (ttmp) REVERT: A 431 MET cc_start: 0.7788 (mtp) cc_final: 0.7061 (mmt) REVERT: A 478 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6715 (ttpt) REVERT: A 488 MET cc_start: 0.8153 (mmp) cc_final: 0.7864 (tpt) REVERT: A 581 LYS cc_start: 0.8521 (tmtt) cc_final: 0.6879 (mmtm) REVERT: A 690 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7744 (mtm110) REVERT: A 702 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8357 (mm-30) REVERT: A 712 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7459 (mtt90) REVERT: A 716 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7240 (tpp-160) REVERT: B 148 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5543 (mpt180) REVERT: B 253 LYS cc_start: 0.8344 (ttmp) cc_final: 0.7682 (mmtt) REVERT: B 431 MET cc_start: 0.7871 (mtp) cc_final: 0.7665 (mtp) REVERT: B 461 TYR cc_start: 0.6732 (t80) cc_final: 0.6502 (t80) REVERT: B 478 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6910 (tmmt) REVERT: B 488 MET cc_start: 0.8212 (mmp) cc_final: 0.7946 (tpt) REVERT: B 641 ASP cc_start: 0.8437 (p0) cc_final: 0.8222 (p0) REVERT: B 690 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7721 (mtm110) REVERT: B 702 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 716 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7194 (tpp-160) REVERT: C 148 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.5412 (mpt180) REVERT: C 167 THR cc_start: 0.8216 (p) cc_final: 0.7892 (t) REVERT: C 253 LYS cc_start: 0.8299 (ttmp) cc_final: 0.7678 (mmtt) REVERT: C 367 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7386 (pt0) REVERT: C 478 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6803 (tmmt) REVERT: C 488 MET cc_start: 0.8188 (mmp) cc_final: 0.7948 (tpt) REVERT: C 687 GLU cc_start: 0.8051 (tp30) cc_final: 0.7097 (tt0) REVERT: C 702 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 716 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7234 (tpp-160) REVERT: C 736 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: D 253 LYS cc_start: 0.8088 (ttmp) cc_final: 0.7664 (mptp) REVERT: D 291 SER cc_start: 0.8911 (m) cc_final: 0.8677 (p) REVERT: D 368 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8154 (ttmt) REVERT: D 431 MET cc_start: 0.7802 (mtp) cc_final: 0.7021 (mmt) REVERT: D 478 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6790 (tmmt) REVERT: D 488 MET cc_start: 0.8192 (mmp) cc_final: 0.7933 (tpt) REVERT: D 581 LYS cc_start: 0.7481 (tppt) cc_final: 0.7160 (mmtm) REVERT: D 686 LYS cc_start: 0.7955 (mttm) cc_final: 0.7733 (mmtt) REVERT: D 690 ARG cc_start: 0.8447 (ptp-110) cc_final: 0.7932 (mtm110) REVERT: D 702 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8315 (mm-30) REVERT: D 716 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7269 (tpm170) REVERT: D 741 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7377 (mp0) outliers start: 43 outliers final: 18 residues processed: 344 average time/residue: 1.4206 time to fit residues: 554.0395 Evaluate side-chains 333 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 712 ARG Chi-restraints excluded: chain B residue 148 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 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS 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 681 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 744 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 681 VAL Chi-restraints excluded: chain D residue 741 GLU 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: 6.9990 chunk 66 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 92 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 279 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 = 0.3966 r_free = 0.3966 target = 0.170525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117809 restraints weight = 26203.972| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.37 r_work: 0.3171 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5230 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= 0.106 Angle : 0.544 7.700 30896 Z= 0.275 Chirality : 0.038 0.162 3308 Planarity : 0.004 0.077 3716 Dihedral : 18.761 109.427 4224 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.63 % Allowed : 19.14 % 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: 0.79 (0.17), residues: 2552 helix: 1.71 (0.13), residues: 1620 sheet: 0.01 (0.48), residues: 112 loop : -1.89 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 710 HIS 0.005 0.001 HIS C 256 PHE 0.013 0.001 PHE B 316 TYR 0.016 0.001 TYR A 461 ARG 0.019 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 942) hydrogen bonds : angle 3.42246 ( 2778) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.28271 ( 8) covalent geometry : bond 0.00244 (23076) covalent geometry : angle 0.54359 (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 341 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.8141 (ttmp) cc_final: 0.7622 (mmtt) REVERT: A 478 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6693 (ttpt) REVERT: A 488 MET cc_start: 0.8055 (mmp) cc_final: 0.7756 (tpt) REVERT: A 690 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7587 (mtm110) REVERT: A 702 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 712 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7373 (mtt90) REVERT: A 716 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7319 (tpm170) REVERT: A 741 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 148 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5495 (mpt180) REVERT: B 253 LYS cc_start: 0.8253 (ttmp) cc_final: 0.7679 (mmtt) REVERT: B 431 MET cc_start: 0.7463 (mtp) cc_final: 0.7211 (mtp) REVERT: B 461 TYR cc_start: 0.6735 (t80) cc_final: 0.6489 (t80) REVERT: B 478 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6881 (tmmt) REVERT: B 488 MET cc_start: 0.8155 (mmp) cc_final: 0.7869 (tpt) REVERT: B 690 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7503 (mtm110) REVERT: B 702 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8104 (mm-30) REVERT: B 716 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7194 (tpp-160) REVERT: C 148 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5406 (mpt180) REVERT: C 167 THR cc_start: 0.8277 (p) cc_final: 0.7898 (t) REVERT: C 202 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7607 (ptt-90) REVERT: C 253 LYS cc_start: 0.8226 (ttmp) cc_final: 0.7653 (mmtt) REVERT: C 367 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7396 (pt0) REVERT: C 478 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6849 (tmmt) REVERT: C 488 MET cc_start: 0.8202 (mmp) cc_final: 0.7949 (tpt) REVERT: C 687 GLU cc_start: 0.7754 (tp30) cc_final: 0.6848 (tm-30) REVERT: C 702 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 716 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7283 (tpp-160) REVERT: C 736 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: D 253 LYS cc_start: 0.7966 (ttmp) cc_final: 0.7649 (mptp) REVERT: D 368 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8103 (ttmt) REVERT: D 431 MET cc_start: 0.7430 (mtp) cc_final: 0.6721 (mmp) REVERT: D 478 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6820 (tmmt) REVERT: D 482 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6488 (pt) REVERT: D 488 MET cc_start: 0.8094 (mmp) cc_final: 0.7822 (tpt) REVERT: D 581 LYS cc_start: 0.7296 (tppt) cc_final: 0.7022 (mmtm) REVERT: D 686 LYS cc_start: 0.7813 (mttm) cc_final: 0.7558 (mttm) REVERT: D 690 ARG cc_start: 0.8261 (ptp-110) cc_final: 0.7758 (mtm110) REVERT: D 702 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 716 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7258 (tpp-160) REVERT: D 738 LYS cc_start: 0.9213 (tttp) cc_final: 0.8994 (tttp) REVERT: D 741 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7259 (mp0) outliers start: 37 outliers final: 21 residues processed: 330 average time/residue: 1.3743 time to fit residues: 516.0146 Evaluate side-chains 331 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 148 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 548 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 368 LYS 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 C residue 740 THR Chi-restraints excluded: chain C residue 744 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 741 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 226 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 643 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116429 restraints weight = 26071.574| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.25 r_work: 0.3148 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.88 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: 36 | |-----------------------------------------------------------------------------| |-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: 34 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23080 Z= 0.138 Angle : 0.583 7.428 30896 Z= 0.292 Chirality : 0.040 0.174 3308 Planarity : 0.004 0.079 3716 Dihedral : 18.895 109.558 4224 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.94 % Allowed : 19.14 % Favored : 78.92 % 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: 0.65 (0.17), residues: 2552 helix: 1.60 (0.13), residues: 1628 sheet: -0.04 (0.48), residues: 112 loop : -1.99 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.013 0.001 PHE B 316 TYR 0.016 0.001 TYR A 461 ARG 0.019 0.001 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 942) hydrogen bonds : angle 3.53197 ( 2778) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.34583 ( 8) covalent geometry : bond 0.00333 (23076) covalent geometry : angle 0.58289 (30888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22291.60 seconds wall clock time: 390 minutes 32.04 seconds (23432.04 seconds total)