Starting phenix.real_space_refine on Sun Oct 12 07:18:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6o_42998/10_2025/8v6o_42998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6o_42998/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v6o_42998/10_2025/8v6o_42998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6o_42998/10_2025/8v6o_42998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v6o_42998/10_2025/8v6o_42998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6o_42998/10_2025/8v6o_42998.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.47, per 1000 atoms: 0.24 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.74 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: 3.63 Time building geometry restraints manager: 2.33 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 905) selection = (chain 'B' and resid 117 through 905) selection = (chain 'C' and resid 117 through 905) selection = (chain 'D' and resid 117 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: 1.120 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.390 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG D 693 TYR 0.012 0.001 TYR A 461 PHE 0.023 0.002 PHE A 633 TRP 0.023 0.002 TRP C 692 HIS 0.008 0.002 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00934 (23076) covalent geometry : angle 1.36096 (30888) SS BOND : bond 0.00971 ( 4) SS BOND : angle 0.47548 ( 8) hydrogen bonds : bond 0.34815 ( 942) hydrogen bonds : angle 9.96759 ( 2778) *********************** 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 : 0.876 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: 0.7016 time to fit residues: 461.3778 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 : 0.840 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 284 HIS A 286 GLN A 314 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 671 ASN B 227 GLN B 274 GLN B 284 HIS B 286 GLN B 314 ASN B 430 HIS B 671 ASN C 284 HIS C 286 GLN C 314 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 227 GLN D 251 ASN D 279 GLN D 284 HIS D 286 GLN D 314 ASN D 580 GLN D 643 ASN D 671 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128071 restraints weight = 26729.994| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.27 r_work: 0.3331 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23080 Z= 0.134 Angle : 0.617 6.315 30896 Z= 0.314 Chirality : 0.039 0.144 3308 Planarity : 0.005 0.054 3716 Dihedral : 23.668 150.220 4226 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.35 % Allowed : 12.52 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.13), residues: 2552 helix: -1.98 (0.10), residues: 1608 sheet: -0.75 (0.43), residues: 112 loop : -3.00 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 690 TYR 0.017 0.002 TYR C 575 PHE 0.023 0.001 PHE C 633 TRP 0.020 0.002 TRP D 692 HIS 0.009 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00300 (23076) covalent geometry : angle 0.61666 (30888) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.20624 ( 8) hydrogen bonds : bond 0.04334 ( 942) hydrogen bonds : angle 4.14863 ( 2778) *********************** 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 459 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 383 time to evaluate : 0.778 Fit side-chains REVERT: A 211 GLU cc_start: 0.8350 (tt0) cc_final: 0.8096 (tt0) REVERT: A 214 GLU cc_start: 0.7373 (tt0) cc_final: 0.7086 (pt0) REVERT: A 431 MET cc_start: 0.7685 (mtp) cc_final: 0.6939 (mmt) REVERT: A 478 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7097 (tmmt) REVERT: A 690 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7561 (mtm110) REVERT: B 129 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: B 159 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6692 (mmp) REVERT: B 202 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7744 (ptm160) REVERT: B 214 GLU cc_start: 0.7445 (tt0) cc_final: 0.7161 (pt0) REVERT: B 478 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7220 (tmmt) REVERT: B 495 MET cc_start: 0.8450 (mtp) cc_final: 0.8168 (mtt) REVERT: B 690 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7585 (mtm110) REVERT: B 702 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 716 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7407 (tpp-160) REVERT: C 210 GLU cc_start: 0.7377 (tp30) cc_final: 0.7151 (tp30) REVERT: C 335 THR cc_start: 0.8645 (m) cc_final: 0.8411 (p) REVERT: C 367 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7505 (pt0) REVERT: C 478 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7223 (tmmt) REVERT: C 687 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7012 (tp30) REVERT: C 690 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7388 (mtm110) REVERT: C 712 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7758 (mtm110) REVERT: C 716 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7449 (tpp-160) REVERT: D 156 ASP cc_start: 0.7642 (t0) cc_final: 0.7078 (p0) REVERT: D 283 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: D 368 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8054 (ttmp) REVERT: D 478 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7137 (tmmt) REVERT: D 581 LYS cc_start: 0.7549 (tppt) cc_final: 0.7086 (mmtt) REVERT: D 672 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7839 (mmt) REVERT: D 686 LYS cc_start: 0.7688 (mttm) cc_final: 0.7451 (mmtt) REVERT: D 687 GLU cc_start: 0.7804 (tp30) cc_final: 0.7599 (tp30) REVERT: D 690 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7805 (mtm110) REVERT: D 716 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7380 (mmt-90) outliers start: 76 outliers final: 16 residues processed: 431 average time/residue: 0.6717 time to fit residues: 328.4084 Evaluate side-chains 337 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 333 LEU 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 732 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 690 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 233 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 284 HIS A 286 GLN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN B 274 GLN B 284 HIS B 286 GLN B 430 HIS C 284 HIS C 286 GLN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 330 ASN D 643 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121230 restraints weight = 26933.817| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.36 r_work: 0.3237 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23080 Z= 0.121 Angle : 0.565 6.285 30896 Z= 0.285 Chirality : 0.038 0.140 3308 Planarity : 0.004 0.054 3716 Dihedral : 22.259 145.862 4224 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.92 % Allowed : 13.45 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.16), residues: 2552 helix: -0.13 (0.13), residues: 1576 sheet: -0.64 (0.44), residues: 112 loop : -2.42 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 371 TYR 0.017 0.002 TYR D 208 PHE 0.015 0.001 PHE B 633 TRP 0.013 0.001 TRP A 692 HIS 0.006 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00276 (23076) covalent geometry : angle 0.56551 (30888) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.41630 ( 8) hydrogen bonds : bond 0.03896 ( 942) hydrogen bonds : angle 3.69749 ( 2778) *********************** 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 421 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 332 time to evaluate : 0.927 Fit side-chains REVERT: A 156 ASP cc_start: 0.7752 (t0) cc_final: 0.7227 (p0) REVERT: A 220 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: A 431 MET cc_start: 0.7635 (mtp) cc_final: 0.6894 (mmt) REVERT: A 478 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7069 (tmmt) REVERT: A 631 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 690 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7628 (mtm110) REVERT: B 159 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6650 (mmp) REVERT: B 160 HIS cc_start: 0.7471 (m-70) cc_final: 0.6955 (m-70) REVERT: B 202 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7875 (ptm160) REVERT: B 327 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7341 (mmm-85) REVERT: B 478 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7238 (tmmt) REVERT: B 631 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 690 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7598 (mtm110) REVERT: B 691 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (pt) REVERT: C 167 THR cc_start: 0.8243 (p) cc_final: 0.7830 (t) REVERT: C 286 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7913 (mp-120) REVERT: C 327 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7141 (mmm160) REVERT: C 367 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7476 (pt0) REVERT: C 478 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7060 (tmmt) REVERT: C 631 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 712 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7776 (mtm110) REVERT: C 716 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7383 (tpp-160) REVERT: D 368 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8129 (ttmp) REVERT: D 431 MET cc_start: 0.7487 (mtp) cc_final: 0.6831 (mmp) REVERT: D 478 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7068 (tmmt) REVERT: D 581 LYS cc_start: 0.7596 (tppt) cc_final: 0.7109 (mmpt) REVERT: D 691 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8381 (mt) REVERT: D 712 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7776 (mtm110) REVERT: D 716 ARG cc_start: 0.8117 (ttp-170) cc_final: 0.7362 (tpp-160) outliers start: 89 outliers final: 13 residues processed: 391 average time/residue: 0.6552 time to fit residues: 291.8054 Evaluate side-chains 313 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 286 GLN 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 536 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 229 ASP 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 691 ILE Chi-restraints excluded: chain D residue 712 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 171 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 186 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114577 restraints weight = 26908.484| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.31 r_work: 0.3149 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23080 Z= 0.207 Angle : 0.670 8.376 30896 Z= 0.330 Chirality : 0.042 0.162 3308 Planarity : 0.005 0.055 3716 Dihedral : 22.339 155.806 4224 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.47 % Rotamer: Outliers : 4.72 % Allowed : 13.71 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2552 helix: 0.40 (0.13), residues: 1580 sheet: -0.60 (0.44), residues: 112 loop : -2.21 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 487 TYR 0.021 0.002 TYR D 208 PHE 0.015 0.002 PHE B 715 TRP 0.013 0.001 TRP B 692 HIS 0.008 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00505 (23076) covalent geometry : angle 0.67020 (30888) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.50685 ( 8) hydrogen bonds : bond 0.04473 ( 942) hydrogen bonds : angle 3.90103 ( 2778) *********************** 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 443 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 336 time to evaluate : 0.745 Fit side-chains REVERT: A 156 ASP cc_start: 0.7734 (t0) cc_final: 0.7186 (p0) REVERT: A 253 LYS cc_start: 0.8221 (ttmp) cc_final: 0.7654 (mmtt) REVERT: A 327 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7143 (mmm160) REVERT: A 431 MET cc_start: 0.7875 (mtp) cc_final: 0.7094 (mmt) REVERT: A 478 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7041 (tmmt) REVERT: A 631 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 690 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7816 (mtm110) REVERT: A 716 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7285 (tpp-160) REVERT: B 156 ASP cc_start: 0.7600 (t0) cc_final: 0.6979 (p0) REVERT: B 159 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6653 (mmp) REVERT: B 253 LYS cc_start: 0.8247 (ttmp) cc_final: 0.7627 (mmtt) REVERT: B 327 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7349 (mmm-85) REVERT: B 478 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7130 (tmmt) REVERT: B 631 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 690 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7832 (mtm110) REVERT: B 716 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7341 (tpm170) REVERT: C 156 ASP cc_start: 0.7574 (t0) cc_final: 0.7244 (p0) REVERT: C 253 LYS cc_start: 0.8229 (ttmp) cc_final: 0.7630 (mmtt) REVERT: C 286 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8277 (mp-120) REVERT: C 327 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7223 (mmm160) REVERT: C 367 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7259 (pt0) REVERT: C 368 LYS cc_start: 0.8321 (mmmm) cc_final: 0.7982 (mptt) REVERT: C 478 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6997 (tmmt) REVERT: C 691 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8399 (pt) REVERT: C 712 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7744 (mtm110) REVERT: C 716 ARG cc_start: 0.8302 (ttp-170) cc_final: 0.7246 (tpm170) REVERT: C 736 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: D 202 ARG cc_start: 0.8314 (ptm160) cc_final: 0.8063 (ptm160) REVERT: D 253 LYS cc_start: 0.8082 (ttmp) cc_final: 0.7631 (mmtt) REVERT: D 291 SER cc_start: 0.8871 (m) cc_final: 0.8541 (p) REVERT: D 368 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8243 (ttmp) REVERT: D 478 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6920 (tmmt) REVERT: D 581 LYS cc_start: 0.7603 (tppt) cc_final: 0.7188 (mmtm) REVERT: D 691 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8643 (mt) REVERT: D 716 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7237 (tpp-160) outliers start: 107 outliers final: 35 residues processed: 408 average time/residue: 0.6797 time to fit residues: 314.7156 Evaluate side-chains 366 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 327 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 726 ASP 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 327 ARG Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 732 LEU 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 357 LEU 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 536 SER Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU 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 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 639 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 38 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 164 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 286 GLN 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 = 0.3926 r_free = 0.3926 target = 0.168320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116434 restraints weight = 26609.318| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.30 r_work: 0.3152 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4725 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= 0.150 Angle : 0.578 6.680 30896 Z= 0.290 Chirality : 0.040 0.147 3308 Planarity : 0.004 0.056 3716 Dihedral : 21.471 147.002 4224 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.59 % Allowed : 15.56 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2552 helix: 0.89 (0.13), residues: 1580 sheet: -0.50 (0.43), residues: 112 loop : -2.09 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 202 TYR 0.021 0.002 TYR D 208 PHE 0.015 0.001 PHE D 316 TRP 0.011 0.002 TRP B 692 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00360 (23076) covalent geometry : angle 0.57847 (30888) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.39485 ( 8) hydrogen bonds : bond 0.03657 ( 942) hydrogen bonds : angle 3.65186 ( 2778) *********************** 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 426 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 322 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 148 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5298 (mpt180) REVERT: A 253 LYS cc_start: 0.8243 (ttmp) cc_final: 0.7693 (mmtt) REVERT: A 327 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7129 (mmm160) REVERT: A 431 MET cc_start: 0.7956 (mtp) cc_final: 0.7189 (mmt) REVERT: A 478 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6962 (tmmt) REVERT: A 642 LEU cc_start: 0.8555 (mt) cc_final: 0.8348 (mt) REVERT: A 690 ARG cc_start: 0.8338 (mtt90) cc_final: 0.7947 (mtm110) REVERT: A 716 ARG cc_start: 0.8302 (ttp-170) cc_final: 0.7346 (tpp-160) REVERT: B 145 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6708 (mt) REVERT: B 253 LYS cc_start: 0.8270 (ttmp) cc_final: 0.7675 (mmtt) REVERT: B 327 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7344 (mmm-85) REVERT: B 431 MET cc_start: 0.7976 (mtp) cc_final: 0.7735 (mtp) REVERT: B 478 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7071 (tmmt) REVERT: B 553 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8095 (mt) REVERT: B 690 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7948 (mtm110) REVERT: B 716 ARG cc_start: 0.8326 (ttp-170) cc_final: 0.7322 (tpp-160) REVERT: C 145 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6854 (mp) REVERT: C 199 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7114 (pp) REVERT: C 253 LYS cc_start: 0.8262 (ttmp) cc_final: 0.7640 (mmtt) REVERT: C 327 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7183 (mmm160) REVERT: C 367 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7295 (pt0) REVERT: C 368 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8041 (mptt) REVERT: C 478 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6909 (tmmt) REVERT: C 553 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8081 (mt) REVERT: C 712 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7777 (mtm110) REVERT: C 716 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.7320 (tpm170) REVERT: C 736 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: D 202 ARG cc_start: 0.8278 (ptm160) cc_final: 0.8007 (ptm160) REVERT: D 253 LYS cc_start: 0.8110 (ttmp) cc_final: 0.7689 (mmtt) REVERT: D 291 SER cc_start: 0.8865 (m) cc_final: 0.8607 (p) REVERT: D 368 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8261 (ttmp) REVERT: D 431 MET cc_start: 0.7996 (mtp) cc_final: 0.7231 (mmt) REVERT: D 478 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6867 (tmmt) REVERT: D 581 LYS cc_start: 0.7707 (tppt) cc_final: 0.7322 (mmtm) REVERT: D 690 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8038 (mtm110) REVERT: D 691 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (mt) REVERT: D 712 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7809 (mtm110) REVERT: D 716 ARG cc_start: 0.8261 (ttp-170) cc_final: 0.7303 (tpm170) outliers start: 104 outliers final: 34 residues processed: 397 average time/residue: 0.6716 time to fit residues: 303.4122 Evaluate side-chains 352 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 145 LEU 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 327 ARG 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 536 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 199 ILE 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 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 553 LEU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 136 VAL 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 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3925 r_free = 0.3925 target = 0.168151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115970 restraints weight = 26731.953| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.29 r_work: 0.3144 rms_B_bonded: 3.13 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: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23080 Z= 0.148 Angle : 0.587 7.437 30896 Z= 0.295 Chirality : 0.040 0.149 3308 Planarity : 0.004 0.056 3716 Dihedral : 20.958 143.176 4224 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.23 % Allowed : 16.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2552 helix: 1.14 (0.13), residues: 1588 sheet: -0.49 (0.44), residues: 112 loop : -2.00 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 487 TYR 0.021 0.002 TYR D 208 PHE 0.015 0.001 PHE B 316 TRP 0.012 0.002 TRP B 692 HIS 0.007 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00357 (23076) covalent geometry : angle 0.58730 (30888) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.34509 ( 8) hydrogen bonds : bond 0.03669 ( 942) hydrogen bonds : angle 3.66601 ( 2778) *********************** 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 417 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 321 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5383 (mpt180) REVERT: A 199 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7127 (pp) REVERT: A 253 LYS cc_start: 0.8282 (ttmp) cc_final: 0.7701 (mmtt) REVERT: A 327 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: A 431 MET cc_start: 0.7993 (mtp) cc_final: 0.7242 (mmp) REVERT: A 478 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6950 (tmmt) REVERT: A 642 LEU cc_start: 0.8586 (mt) cc_final: 0.8355 (mt) REVERT: A 690 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7934 (mtm110) REVERT: A 716 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7343 (tpp-160) REVERT: B 159 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6730 (mmp) REVERT: B 253 LYS cc_start: 0.8293 (ttmp) cc_final: 0.7704 (mmtt) REVERT: B 327 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7440 (mmm-85) REVERT: B 431 MET cc_start: 0.7965 (mtp) cc_final: 0.7709 (mtp) REVERT: B 478 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7003 (tmmt) REVERT: B 690 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7921 (mtm110) REVERT: B 716 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7275 (tpp-160) REVERT: C 133 GLU cc_start: 0.8360 (mp0) cc_final: 0.8131 (mp0) REVERT: C 253 LYS cc_start: 0.8302 (ttmp) cc_final: 0.7682 (mmtt) REVERT: C 327 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7262 (mmm160) REVERT: C 367 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7373 (pt0) REVERT: C 368 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8052 (mptt) REVERT: C 478 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6857 (tmmt) REVERT: C 631 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 687 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7528 (tm-30) REVERT: C 712 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7745 (mtm110) REVERT: C 716 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7221 (tpp-160) REVERT: C 736 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: D 202 ARG cc_start: 0.8262 (ptm160) cc_final: 0.7966 (ptm160) REVERT: D 253 LYS cc_start: 0.8098 (ttmp) cc_final: 0.7692 (mmtt) REVERT: D 291 SER cc_start: 0.8900 (m) cc_final: 0.8653 (p) REVERT: D 368 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8217 (ttmp) REVERT: D 431 MET cc_start: 0.7989 (mtp) cc_final: 0.7208 (mmt) REVERT: D 478 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6796 (tmmt) REVERT: D 581 LYS cc_start: 0.7725 (tppt) cc_final: 0.7150 (mmpt) REVERT: D 690 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8058 (mtm110) REVERT: D 691 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 712 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7832 (mtm110) REVERT: D 716 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7349 (tpm170) REVERT: D 741 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7457 (mp0) outliers start: 96 outliers final: 42 residues processed: 388 average time/residue: 0.6753 time to fit residues: 297.5512 Evaluate side-chains 364 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 199 ILE 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 357 LEU 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 732 LEU Chi-restraints excluded: chain A residue 744 THR 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 327 ARG Chi-restraints excluded: chain B residue 357 LEU 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 536 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 744 THR 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 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 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 732 LEU 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 165 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 741 GLU Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 160 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117372 restraints weight = 26835.171| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.29 r_work: 0.3164 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 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 = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23080 Z= 0.118 Angle : 0.547 8.430 30896 Z= 0.277 Chirality : 0.038 0.153 3308 Planarity : 0.004 0.057 3716 Dihedral : 20.425 135.908 4224 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.48 % Allowed : 17.55 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2552 helix: 1.35 (0.13), residues: 1596 sheet: -0.40 (0.44), residues: 112 loop : -2.01 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.020 0.001 TYR D 208 PHE 0.015 0.001 PHE D 316 TRP 0.012 0.002 TRP D 521 HIS 0.008 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00280 (23076) covalent geometry : angle 0.54703 (30888) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.28874 ( 8) hydrogen bonds : bond 0.03275 ( 942) hydrogen bonds : angle 3.53220 ( 2778) *********************** 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 396 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6891 (mp) REVERT: A 148 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5492 (mpt180) REVERT: A 253 LYS cc_start: 0.8284 (ttmp) cc_final: 0.7690 (mmtt) REVERT: A 327 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7187 (mmm160) REVERT: A 431 MET cc_start: 0.7891 (mtp) cc_final: 0.7105 (mmp) REVERT: A 478 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6938 (tmmt) REVERT: A 641 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8134 (p0) REVERT: A 642 LEU cc_start: 0.8516 (mt) cc_final: 0.8224 (mt) REVERT: A 690 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7863 (mtm110) REVERT: A 702 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8396 (mm-30) REVERT: A 716 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7307 (tpp-160) REVERT: B 159 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6764 (mmp) REVERT: B 253 LYS cc_start: 0.8318 (ttmp) cc_final: 0.7696 (mmtt) REVERT: B 327 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7272 (mmm-85) REVERT: B 431 MET cc_start: 0.7882 (mtp) cc_final: 0.7606 (mtp) REVERT: B 478 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6982 (tmmt) REVERT: B 581 LYS cc_start: 0.8525 (tmtt) cc_final: 0.6903 (mmtm) REVERT: B 690 ARG cc_start: 0.8258 (mtt90) cc_final: 0.7866 (mtm110) REVERT: B 716 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.7252 (tpp-160) REVERT: C 253 LYS cc_start: 0.8317 (ttmp) cc_final: 0.7670 (mmtt) REVERT: C 327 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7230 (mmm160) REVERT: C 367 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7347 (pt0) REVERT: C 368 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8037 (mptt) REVERT: C 478 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6839 (tmmt) REVERT: C 488 MET cc_start: 0.8290 (mmp) cc_final: 0.8063 (tpt) REVERT: C 631 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: C 687 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7398 (tm-30) REVERT: C 691 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8254 (pt) REVERT: C 702 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 716 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7235 (tpp-160) REVERT: C 736 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: D 202 ARG cc_start: 0.8261 (ptm160) cc_final: 0.7969 (ptm160) REVERT: D 253 LYS cc_start: 0.8098 (ttmp) cc_final: 0.7682 (mmtt) REVERT: D 291 SER cc_start: 0.8874 (m) cc_final: 0.8627 (p) REVERT: D 368 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8230 (ttmp) REVERT: D 431 MET cc_start: 0.7919 (mtp) cc_final: 0.7104 (mmt) REVERT: D 478 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6778 (tmmt) REVERT: D 581 LYS cc_start: 0.7633 (tppt) cc_final: 0.7254 (mmtm) REVERT: D 690 ARG cc_start: 0.8440 (ptp-110) cc_final: 0.7991 (mtm110) REVERT: D 691 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8530 (mt) REVERT: D 702 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 712 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7789 (mtm110) REVERT: D 716 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7292 (tpp-160) outliers start: 79 outliers final: 42 residues processed: 369 average time/residue: 0.7109 time to fit residues: 297.0611 Evaluate side-chains 365 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 307 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 357 LEU 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 641 ASP Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 744 THR 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 327 ARG Chi-restraints excluded: chain B residue 357 LEU 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 536 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 744 THR 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 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 639 LEU Chi-restraints excluded: chain C residue 691 ILE 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 165 SER Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 4 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 160 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.171050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119404 restraints weight = 26723.284| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.30 r_work: 0.3216 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23080 Z= 0.098 Angle : 0.528 7.462 30896 Z= 0.267 Chirality : 0.038 0.145 3308 Planarity : 0.004 0.056 3716 Dihedral : 19.667 124.948 4224 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.31 % Allowed : 18.30 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2552 helix: 1.49 (0.13), residues: 1624 sheet: -0.26 (0.45), residues: 112 loop : -2.04 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 202 TYR 0.018 0.001 TYR D 208 PHE 0.014 0.001 PHE B 316 TRP 0.013 0.002 TRP C 692 HIS 0.009 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00223 (23076) covalent geometry : angle 0.52829 (30888) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.22110 ( 8) hydrogen bonds : bond 0.02891 ( 942) hydrogen bonds : angle 3.40500 ( 2778) *********************** 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 399 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 324 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 148 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5549 (mpt180) REVERT: A 253 LYS cc_start: 0.8301 (ttmp) cc_final: 0.7685 (mmtt) REVERT: A 327 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7148 (mmm160) REVERT: A 431 MET cc_start: 0.7787 (mtp) cc_final: 0.7058 (mmt) REVERT: A 478 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6852 (tmmt) REVERT: A 581 LYS cc_start: 0.8466 (tmtt) cc_final: 0.6843 (mmtm) REVERT: A 642 LEU cc_start: 0.8418 (mt) cc_final: 0.8197 (mt) REVERT: A 690 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7823 (mtm110) REVERT: A 702 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 716 ARG cc_start: 0.8273 (ttp-170) cc_final: 0.7252 (tpp-160) REVERT: B 253 LYS cc_start: 0.8334 (ttmp) cc_final: 0.7691 (mmtt) REVERT: B 368 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7728 (ttmp) REVERT: B 431 MET cc_start: 0.7844 (mtp) cc_final: 0.7556 (mtp) REVERT: B 478 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6888 (tmmt) REVERT: B 641 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 690 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7787 (mtm110) REVERT: B 702 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 716 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7241 (tpp-160) REVERT: C 167 THR cc_start: 0.8186 (p) cc_final: 0.7822 (t) REVERT: C 253 LYS cc_start: 0.8340 (ttmp) cc_final: 0.7668 (mmtt) REVERT: C 327 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: C 367 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7385 (pt0) REVERT: C 368 LYS cc_start: 0.8334 (mmmm) cc_final: 0.8123 (ttmt) REVERT: C 478 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6786 (tmmt) REVERT: C 488 MET cc_start: 0.8276 (mmp) cc_final: 0.8069 (tpt) REVERT: C 687 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7329 (tm-30) REVERT: C 702 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 712 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7604 (mtm110) REVERT: C 716 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7197 (tpp-160) REVERT: C 736 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: D 202 ARG cc_start: 0.8218 (ptm160) cc_final: 0.7930 (ptm160) REVERT: D 253 LYS cc_start: 0.8121 (ttmp) cc_final: 0.7672 (mmtt) REVERT: D 291 SER cc_start: 0.8885 (m) cc_final: 0.8638 (p) REVERT: D 368 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8116 (ttmp) REVERT: D 431 MET cc_start: 0.7808 (mtp) cc_final: 0.6979 (mmt) REVERT: D 478 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6798 (tmmt) REVERT: D 581 LYS cc_start: 0.7571 (tppt) cc_final: 0.7193 (mmtm) REVERT: D 690 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.7961 (mtm110) REVERT: D 702 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8294 (mm-30) REVERT: D 712 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7672 (mtm110) REVERT: D 716 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7244 (tpp-160) outliers start: 75 outliers final: 26 residues processed: 374 average time/residue: 0.6685 time to fit residues: 284.1956 Evaluate side-chains 347 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 309 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 229 ASP Chi-restraints excluded: chain A residue 327 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 740 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 357 LEU 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 641 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 744 THR 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 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 712 ARG 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 165 SER Chi-restraints excluded: chain D residue 323 MET 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 641 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 203 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 252 optimal weight: 0.2980 chunk 229 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 160 HIS 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 = 0.3977 r_free = 0.3977 target = 0.171633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120950 restraints weight = 26156.488| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.27 r_work: 0.3212 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.5194 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= 0.092 Angle : 0.518 7.688 30896 Z= 0.262 Chirality : 0.038 0.163 3308 Planarity : 0.004 0.056 3716 Dihedral : 18.939 115.202 4224 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.29 % Allowed : 19.36 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2552 helix: 1.59 (0.13), residues: 1648 sheet: -0.19 (0.46), residues: 112 loop : -2.09 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 202 TYR 0.017 0.001 TYR D 208 PHE 0.013 0.001 PHE B 316 TRP 0.014 0.002 TRP C 710 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00205 (23076) covalent geometry : angle 0.51854 (30888) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.24825 ( 8) hydrogen bonds : bond 0.02718 ( 942) hydrogen bonds : angle 3.31668 ( 2778) *********************** 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 372 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 148 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5606 (mpt180) REVERT: A 253 LYS cc_start: 0.8250 (ttmp) cc_final: 0.7681 (mmtt) REVERT: A 327 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7231 (mmm160) REVERT: A 478 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6789 (ttpt) REVERT: A 642 LEU cc_start: 0.8276 (mt) cc_final: 0.8062 (mt) REVERT: A 690 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7775 (mtm110) REVERT: A 702 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 716 ARG cc_start: 0.8301 (ttp-170) cc_final: 0.7216 (tpp-160) REVERT: B 253 LYS cc_start: 0.8312 (ttmp) cc_final: 0.7679 (mmtt) REVERT: B 368 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7728 (ttmp) REVERT: B 431 MET cc_start: 0.7774 (mtp) cc_final: 0.7499 (mtp) REVERT: B 478 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6938 (tmmt) REVERT: B 690 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7748 (mtm110) REVERT: B 702 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 716 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7198 (tpm170) REVERT: B 750 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (m-40) REVERT: C 167 THR cc_start: 0.8192 (p) cc_final: 0.7883 (t) REVERT: C 253 LYS cc_start: 0.8295 (ttmp) cc_final: 0.7674 (mmtt) REVERT: C 367 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7441 (pt0) REVERT: C 478 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6861 (tmmt) REVERT: C 687 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 702 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8282 (mm-30) REVERT: C 712 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7565 (mtm110) REVERT: C 716 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7198 (tpp-160) REVERT: C 736 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: D 253 LYS cc_start: 0.8079 (ttmp) cc_final: 0.7674 (mmtt) REVERT: D 291 SER cc_start: 0.8881 (m) cc_final: 0.8638 (p) REVERT: D 368 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8101 (ttmp) REVERT: D 431 MET cc_start: 0.7772 (mtp) cc_final: 0.6970 (mmt) REVERT: D 478 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6813 (tmmt) REVERT: D 581 LYS cc_start: 0.7470 (tppt) cc_final: 0.7110 (mmtm) REVERT: D 690 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.7967 (mtm110) REVERT: D 702 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8337 (mm-30) REVERT: D 712 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7662 (mtm110) REVERT: D 716 ARG cc_start: 0.8250 (ttp-170) cc_final: 0.7183 (tpp-160) outliers start: 52 outliers final: 18 residues processed: 352 average time/residue: 0.6853 time to fit residues: 274.4071 Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 536 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 750 ASN 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 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 165 SER 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 712 ARG Chi-restraints excluded: chain D residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 186 optimal weight: 0.7980 chunk 16 optimal weight: 0.0570 chunk 35 optimal weight: 0.1980 chunk 230 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 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 = 0.3969 r_free = 0.3969 target = 0.170775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119861 restraints weight = 26141.207| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.27 r_work: 0.3196 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23080 Z= 0.100 Angle : 0.537 7.092 30896 Z= 0.270 Chirality : 0.038 0.159 3308 Planarity : 0.004 0.056 3716 Dihedral : 18.628 108.246 4224 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.72 % Allowed : 20.24 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2552 helix: 1.61 (0.13), residues: 1648 sheet: -0.17 (0.46), residues: 112 loop : -2.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 202 TYR 0.016 0.001 TYR D 208 PHE 0.014 0.001 PHE B 316 TRP 0.016 0.001 TRP C 710 HIS 0.009 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00230 (23076) covalent geometry : angle 0.53747 (30888) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.27817 ( 8) hydrogen bonds : bond 0.02873 ( 942) hydrogen bonds : angle 3.36134 ( 2778) ********************** 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 353 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6844 (mp) REVERT: A 148 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5672 (mpt180) REVERT: A 253 LYS cc_start: 0.8208 (ttmp) cc_final: 0.7657 (mmtt) REVERT: A 327 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7241 (mmm160) REVERT: A 431 MET cc_start: 0.7811 (mtm) cc_final: 0.6996 (mmp) REVERT: A 478 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6754 (ttpt) REVERT: A 642 LEU cc_start: 0.8298 (mt) cc_final: 0.8088 (mt) REVERT: A 690 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7768 (mtm110) REVERT: A 702 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 716 ARG cc_start: 0.8293 (ttp-170) cc_final: 0.7258 (tpp-160) REVERT: B 253 LYS cc_start: 0.8347 (ttmp) cc_final: 0.7698 (mmtt) REVERT: B 368 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7691 (ttmp) REVERT: B 431 MET cc_start: 0.7788 (mtp) cc_final: 0.7526 (mtp) REVERT: B 478 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6905 (tmmt) REVERT: B 690 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7710 (mtm110) REVERT: B 702 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8344 (mm-30) REVERT: B 716 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7221 (tpp-160) REVERT: C 167 THR cc_start: 0.8233 (p) cc_final: 0.7932 (t) REVERT: C 202 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7606 (tmm-80) REVERT: C 253 LYS cc_start: 0.8268 (ttmp) cc_final: 0.7660 (mmtt) REVERT: C 367 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7431 (pt0) REVERT: C 368 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8035 (ttmt) REVERT: C 478 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6784 (tmmt) REVERT: C 488 MET cc_start: 0.8130 (mmp) cc_final: 0.7853 (tpt) REVERT: C 687 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 702 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 712 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7520 (mtm110) REVERT: C 716 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7210 (tpp-160) REVERT: C 736 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: D 253 LYS cc_start: 0.8079 (ttmp) cc_final: 0.7668 (mmtt) REVERT: D 291 SER cc_start: 0.8891 (m) cc_final: 0.8653 (p) REVERT: D 368 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8111 (ttmt) REVERT: D 431 MET cc_start: 0.7782 (mtp) cc_final: 0.6985 (mmt) REVERT: D 478 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6828 (tmmt) REVERT: D 482 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6428 (pt) REVERT: D 581 LYS cc_start: 0.7467 (tppt) cc_final: 0.7129 (mmtm) REVERT: D 690 ARG cc_start: 0.8449 (ptp-110) cc_final: 0.7975 (mtm110) REVERT: D 702 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 712 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7674 (mtm110) REVERT: D 716 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7185 (tpp-160) outliers start: 39 outliers final: 17 residues processed: 341 average time/residue: 0.6967 time to fit residues: 269.7904 Evaluate side-chains 333 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 536 SER Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 740 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 C residue 158 LEU 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 712 ARG 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 165 SER Chi-restraints excluded: chain D residue 323 MET 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 712 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114656 restraints weight = 26177.671| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.36 r_work: 0.3132 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23080 Z= 0.152 Angle : 0.602 7.506 30896 Z= 0.299 Chirality : 0.041 0.186 3308 Planarity : 0.004 0.056 3716 Dihedral : 18.976 108.165 4224 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.98 % Allowed : 20.06 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2552 helix: 1.49 (0.13), residues: 1628 sheet: -0.19 (0.47), residues: 112 loop : -2.07 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 202 TYR 0.019 0.002 TYR D 208 PHE 0.013 0.001 PHE A 316 TRP 0.017 0.002 TRP C 710 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00368 (23076) covalent geometry : angle 0.60236 (30888) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.38474 ( 8) hydrogen bonds : bond 0.03618 ( 942) hydrogen bonds : angle 3.57498 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10311.37 seconds wall clock time: 175 minutes 33.11 seconds (10533.11 seconds total)