Starting phenix.real_space_refine on Sat Jul 4 17:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6o_42998/07_2026/8v6o_42998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6o_42998/07_2026/8v6o_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_42998/07_2026/8v6o_42998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6o_42998/07_2026/8v6o_42998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v6o_42998/07_2026/8v6o_42998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6o_42998/07_2026/8v6o_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-dev-6108/lib/python3.11/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, 502 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'FZ4': 2, 'POV': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 2 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, 450 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'FZ4': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 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: 5.36, 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: 1.88 Conformation dependent library (CDL) restraints added in 973.9 milliseconds 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: 0.62 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: 3.76 Time building geometry restraints manager: 2.52 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: 1.110 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: 0.050 Process input model: 20.590 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 are 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/Z covalent geometry : bond 0.00934 / 0.47 (23076) covalent geometry : angle 1.36096 / 0.64 (30888) SS BOND : bond 0.00971 / 0.48 ( 4) SS BOND : angle 0.47548 / 0.28 ( 8) hydrogen bonds : bond 0.34815 / 22.82 ( 942) hydrogen bonds : angle 9.96759 / 6.80 ( 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 : 0.892 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: 0.6801 time to fit residues: 449.9359 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 : 0.745 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4052 r_free = 0.4052 target = 0.180217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129270 restraints weight = 26718.816| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.27 r_work: 0.3322 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23080 Z= 0.128 Angle : 0.607 6.388 30896 Z= 0.311 Chirality : 0.039 0.141 3308 Planarity : 0.005 0.054 3716 Dihedral : 23.754 149.681 4226 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.26 % Allowed : 12.74 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.13), residues: 2552 helix: -1.99 (0.10), residues: 1608 sheet: -0.68 (0.43), residues: 112 loop : -3.03 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 690 TYR 0.016 0.002 TYR B 359 PHE 0.021 0.001 PHE C 633 TRP 0.019 0.001 TRP D 692 HIS 0.010 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (23076) covalent geometry : angle 0.60751 / 0.31 (30888) SS BOND : bond 0.00101 / 0.05 ( 4) SS BOND : angle 0.26930 / 0.15 ( 8) hydrogen bonds : bond 0.04630 / 3.04 ( 942) hydrogen bonds : angle 4.16613 / 2.82 ( 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 462 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 388 time to evaluate : 0.846 Fit side-chains REVERT: A 214 GLU cc_start: 0.7330 (tt0) cc_final: 0.7036 (pt0) REVERT: A 431 MET cc_start: 0.7711 (mtp) cc_final: 0.6990 (mmt) REVERT: A 478 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7096 (tmmt) REVERT: A 690 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7544 (mtm110) REVERT: B 129 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: B 159 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6884 (mmp) REVERT: B 214 GLU cc_start: 0.7401 (tt0) cc_final: 0.7118 (pt0) REVERT: B 478 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7209 (tmmt) REVERT: B 495 MET cc_start: 0.8464 (mtp) cc_final: 0.8183 (mtt) REVERT: B 656 PHE cc_start: 0.7320 (m-80) cc_final: 0.7063 (m-80) REVERT: B 690 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7543 (mtm110) REVERT: B 702 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 716 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7400 (tpp-160) REVERT: C 121 LYS cc_start: 0.8022 (mptt) cc_final: 0.7472 (pttm) REVERT: C 210 GLU cc_start: 0.7321 (tp30) cc_final: 0.7052 (tp30) REVERT: C 214 GLU cc_start: 0.7462 (tt0) cc_final: 0.7133 (pt0) REVERT: C 367 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7510 (pt0) REVERT: C 478 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7225 (tmmt) REVERT: C 687 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6984 (tp30) REVERT: C 690 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7377 (mtm110) REVERT: C 712 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (mtm110) REVERT: C 716 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7448 (tpp-160) REVERT: D 156 ASP cc_start: 0.7677 (t0) cc_final: 0.7072 (p0) REVERT: D 283 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: D 368 LYS cc_start: 0.8273 (mmmm) cc_final: 0.8021 (ttmp) REVERT: D 478 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7168 (tmmt) REVERT: D 672 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: D 712 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8040 (mtt90) REVERT: D 716 ARG cc_start: 0.8055 (ttp-170) cc_final: 0.7374 (mmt-90) outliers start: 74 outliers final: 17 residues processed: 436 average time/residue: 0.6676 time to fit residues: 331.5758 Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 318 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 398 THR 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 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: 0.6980 chunk 95 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 330 ASN D 643 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118573 restraints weight = 26909.930| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.36 r_work: 0.3207 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: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 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 = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23080 Z= 0.153 Angle : 0.616 6.390 30896 Z= 0.307 Chirality : 0.040 0.148 3308 Planarity : 0.004 0.054 3716 Dihedral : 22.582 149.891 4224 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 4.10 % Allowed : 13.54 % Favored : 82.36 % 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 are not related in a simple way. whole: -1.52 (0.16), residues: 2552 helix: -0.24 (0.13), residues: 1576 sheet: -0.70 (0.43), residues: 112 loop : -2.43 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 371 TYR 0.017 0.002 TYR C 451 PHE 0.018 0.001 PHE B 633 TRP 0.015 0.001 TRP D 692 HIS 0.007 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (23076) covalent geometry : angle 0.61580 / 0.31 (30888) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 0.45560 / 0.27 ( 8) hydrogen bonds : bond 0.04325 / 2.83 ( 942) hydrogen bonds : angle 3.81781 / 2.59 ( 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 437 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 344 time to evaluate : 0.848 Fit side-chains REVERT: A 156 ASP cc_start: 0.7761 (t0) cc_final: 0.7256 (p0) REVERT: A 431 MET cc_start: 0.7969 (mtp) cc_final: 0.7143 (mmt) REVERT: A 457 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 478 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7092 (tmmt) REVERT: A 631 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 686 LYS cc_start: 0.7606 (mttm) cc_final: 0.7403 (mmtt) REVERT: A 690 ARG cc_start: 0.8437 (mtt90) cc_final: 0.7847 (mtm110) REVERT: A 691 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (pt) REVERT: A 716 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7393 (tpp-160) REVERT: B 156 ASP cc_start: 0.7703 (t0) cc_final: 0.7042 (p0) REVERT: B 159 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6498 (mmp) REVERT: B 202 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7782 (ptm160) REVERT: B 431 MET cc_start: 0.7947 (mtm) cc_final: 0.7668 (mtp) REVERT: B 478 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7265 (tmmt) REVERT: B 631 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 690 ARG cc_start: 0.8409 (mtt90) cc_final: 0.7836 (mtm110) REVERT: B 691 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8278 (pt) REVERT: B 716 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7303 (tpp-160) REVERT: C 327 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7192 (mmm160) REVERT: C 367 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7369 (pt0) REVERT: C 478 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7141 (tmmt) REVERT: C 631 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: C 691 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8250 (pt) REVERT: C 712 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7782 (mtm110) REVERT: C 716 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.7266 (tpp-160) REVERT: D 368 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8251 (ttmp) REVERT: D 431 MET cc_start: 0.7833 (mtp) cc_final: 0.7047 (mmt) REVERT: D 478 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7106 (tmmt) REVERT: D 581 LYS cc_start: 0.7584 (tppt) cc_final: 0.7171 (mmpt) REVERT: D 690 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7961 (mtm110) REVERT: D 716 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7276 (tpp-160) outliers start: 93 outliers final: 16 residues processed: 403 average time/residue: 0.6595 time to fit residues: 303.0747 Evaluate side-chains 330 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 457 LEU 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 691 ILE Chi-restraints excluded: chain B residue 159 MET 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 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 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 691 ILE 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 690 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 171 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 279 GLN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116995 restraints weight = 26905.452| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.32 r_work: 0.3179 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 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 = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.4394 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= 0.158 Angle : 0.603 6.894 30896 Z= 0.301 Chirality : 0.040 0.153 3308 Planarity : 0.004 0.055 3716 Dihedral : 21.932 150.039 4224 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.50 % Allowed : 14.24 % Favored : 81.26 % 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 are not related in a simple way. whole: -0.89 (0.16), residues: 2552 helix: 0.31 (0.13), residues: 1628 sheet: -0.53 (0.43), residues: 112 loop : -2.42 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.021 0.002 TYR C 461 PHE 0.013 0.001 PHE C 316 TRP 0.012 0.001 TRP B 692 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23076) covalent geometry : angle 0.60353 / 0.30 (30888) SS BOND : bond 0.00208 / 0.10 ( 4) SS BOND : angle 0.42942 / 0.26 ( 8) hydrogen bonds : bond 0.03896 / 2.54 ( 942) hydrogen bonds : angle 3.74447 / 2.54 ( 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 436 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 334 time to evaluate : 0.701 Fit side-chains REVERT: A 156 ASP cc_start: 0.7708 (t0) cc_final: 0.7146 (p0) REVERT: A 253 LYS cc_start: 0.8169 (ttmp) cc_final: 0.7609 (mmtt) REVERT: A 327 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7116 (mmm160) REVERT: A 431 MET cc_start: 0.7903 (mtp) cc_final: 0.7121 (mmt) REVERT: A 478 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7043 (tmmt) REVERT: A 631 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 686 LYS cc_start: 0.7776 (mttm) cc_final: 0.7561 (mmtt) REVERT: A 690 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7842 (mtm110) REVERT: A 716 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7298 (tpp-160) REVERT: B 156 ASP cc_start: 0.7502 (t0) cc_final: 0.7019 (p0) REVERT: B 159 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6701 (mmp) REVERT: B 253 LYS cc_start: 0.8240 (ttmp) cc_final: 0.7653 (mmtt) REVERT: B 327 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7088 (mmm-85) REVERT: B 478 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7180 (tmmt) REVERT: B 631 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 690 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7850 (mtm110) REVERT: B 716 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.7313 (tpp-160) REVERT: C 156 ASP cc_start: 0.7583 (t0) cc_final: 0.7181 (p0) REVERT: C 327 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7114 (mmm160) REVERT: C 367 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7310 (pt0) REVERT: C 368 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7972 (mptt) REVERT: C 478 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6958 (tmmt) REVERT: C 691 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (pt) REVERT: C 712 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7802 (mtm110) REVERT: C 716 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7319 (tpm170) REVERT: C 736 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: D 202 ARG cc_start: 0.8293 (ptm160) cc_final: 0.8050 (ptm160) REVERT: D 253 LYS cc_start: 0.8065 (ttmp) cc_final: 0.7640 (mptp) REVERT: D 291 SER cc_start: 0.8895 (m) cc_final: 0.8592 (p) REVERT: D 368 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8230 (ttmp) REVERT: D 431 MET cc_start: 0.7880 (mtp) cc_final: 0.7105 (mmt) REVERT: D 478 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6948 (tmmt) REVERT: D 581 LYS cc_start: 0.7526 (tppt) cc_final: 0.7110 (mmpt) REVERT: D 690 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7949 (mtm110) REVERT: D 712 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7804 (mtm110) REVERT: D 716 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7327 (tpp-160) outliers start: 102 outliers final: 31 residues processed: 399 average time/residue: 0.6609 time to fit residues: 300.9886 Evaluate side-chains 361 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 398 THR 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 B residue 158 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 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 536 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 639 LEU 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 536 SER Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU 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 536 SER Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 712 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 38 optimal weight: 9.9990 chunk 100 optimal weight: 0.0030 chunk 245 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118370 restraints weight = 26599.960| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.32 r_work: 0.3203 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23080 Z= 0.118 Angle : 0.544 6.205 30896 Z= 0.275 Chirality : 0.038 0.144 3308 Planarity : 0.004 0.056 3716 Dihedral : 21.063 146.603 4224 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.66 % Allowed : 16.31 % Favored : 80.03 % 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 are not related in a simple way. whole: -0.29 (0.17), residues: 2552 helix: 0.83 (0.13), residues: 1636 sheet: -0.34 (0.44), residues: 112 loop : -2.32 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 202 TYR 0.025 0.002 TYR C 461 PHE 0.013 0.001 PHE D 316 TRP 0.011 0.001 TRP B 692 HIS 0.007 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (23076) covalent geometry : angle 0.54358 / 0.27 (30888) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 0.33553 / 0.20 ( 8) hydrogen bonds : bond 0.03313 / 2.15 ( 942) hydrogen bonds : angle 3.54569 / 2.40 ( 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 408 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 325 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 253 LYS cc_start: 0.8243 (ttmp) cc_final: 0.7686 (mmtt) REVERT: A 327 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7107 (mmm160) REVERT: A 368 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7807 (ttmt) REVERT: A 431 MET cc_start: 0.7866 (mtp) cc_final: 0.7065 (mmt) REVERT: A 478 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7052 (tmmt) REVERT: A 631 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 686 LYS cc_start: 0.7757 (mttm) cc_final: 0.7522 (mmtt) REVERT: A 690 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7856 (mtm110) REVERT: A 716 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7290 (tpp-160) REVERT: B 253 LYS cc_start: 0.8249 (ttmp) cc_final: 0.7636 (mmtt) REVERT: B 368 LYS cc_start: 0.8143 (mptt) cc_final: 0.7877 (ttmp) REVERT: B 431 MET cc_start: 0.7913 (mtp) cc_final: 0.7655 (mtp) REVERT: B 478 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7039 (tmmt) REVERT: B 631 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: B 641 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8146 (p0) REVERT: B 690 ARG cc_start: 0.8321 (mtt90) cc_final: 0.7875 (mtm110) REVERT: B 716 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.7285 (tpp-160) REVERT: C 156 ASP cc_start: 0.7485 (t0) cc_final: 0.7145 (p0) REVERT: C 167 THR cc_start: 0.8148 (p) cc_final: 0.7819 (t) REVERT: C 199 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7048 (pp) REVERT: C 253 LYS cc_start: 0.8196 (ttmp) cc_final: 0.7604 (mmtt) REVERT: C 327 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7091 (mmm160) REVERT: C 367 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7329 (pt0) REVERT: C 368 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8019 (mptt) REVERT: C 478 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6929 (tmmt) REVERT: C 553 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 716 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.7242 (tpp-160) REVERT: C 736 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: D 148 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5868 (mpt90) REVERT: D 202 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7965 (ptm160) REVERT: D 253 LYS cc_start: 0.8099 (ttmp) cc_final: 0.7671 (mmtt) REVERT: D 291 SER cc_start: 0.8892 (m) cc_final: 0.8605 (p) REVERT: D 368 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8184 (ttmp) REVERT: D 431 MET cc_start: 0.7881 (mtp) cc_final: 0.7118 (mmt) REVERT: D 478 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6885 (tmmt) REVERT: D 581 LYS cc_start: 0.7545 (tppt) cc_final: 0.7101 (mmpt) REVERT: D 690 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7959 (mtm110) REVERT: D 712 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7798 (mtm110) REVERT: D 716 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.7358 (tpm170) outliers start: 83 outliers final: 24 residues processed: 381 average time/residue: 0.6760 time to fit residues: 293.5839 Evaluate side-chains 336 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 631 GLU Chi-restraints excluded: chain A residue 681 VAL 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 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 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 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 736 GLU Chi-restraints excluded: chain D residue 148 ARG 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 478 LYS Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 712 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 330 ASN D 643 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120467 restraints weight = 26754.994| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.30 r_work: 0.3205 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23080 Z= 0.098 Angle : 0.517 5.885 30896 Z= 0.262 Chirality : 0.038 0.143 3308 Planarity : 0.004 0.056 3716 Dihedral : 20.127 142.732 4224 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.75 % Allowed : 16.62 % Favored : 79.63 % 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 are not related in a simple way. whole: 0.18 (0.17), residues: 2552 helix: 1.23 (0.13), residues: 1628 sheet: -0.23 (0.44), residues: 112 loop : -2.18 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 188 TYR 0.018 0.001 TYR D 208 PHE 0.013 0.001 PHE C 316 TRP 0.011 0.001 TRP B 481 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (23076) covalent geometry : angle 0.51713 / 0.26 (30888) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.24859 / 0.16 ( 8) hydrogen bonds : bond 0.02937 / 1.90 ( 942) hydrogen bonds : angle 3.42245 / 2.31 ( 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 421 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 336 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6926 (mp) REVERT: A 148 ARG cc_start: 0.5641 (OUTLIER) cc_final: 0.5357 (mpt180) REVERT: A 199 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 202 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7720 (ptm160) REVERT: A 253 LYS cc_start: 0.8206 (ttmp) cc_final: 0.7654 (mmtt) REVERT: A 327 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7130 (mmm160) REVERT: A 368 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7724 (ttmt) REVERT: A 431 MET cc_start: 0.7796 (mtp) cc_final: 0.7019 (mmt) REVERT: A 478 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6955 (ttpt) REVERT: A 631 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 686 LYS cc_start: 0.7649 (mttm) cc_final: 0.7347 (mmtt) REVERT: A 690 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7753 (mtm110) REVERT: A 702 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 716 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7234 (tpp-160) REVERT: B 145 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6782 (mp) REVERT: B 159 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6454 (mmp) REVERT: B 202 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7701 (ptm160) REVERT: B 253 LYS cc_start: 0.8256 (ttmp) cc_final: 0.7619 (mmtt) REVERT: B 368 LYS cc_start: 0.8057 (mptt) cc_final: 0.7775 (ttmp) REVERT: B 431 MET cc_start: 0.7843 (mtp) cc_final: 0.7598 (mtp) REVERT: B 478 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7007 (tmmt) REVERT: B 631 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 690 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7789 (mtm110) REVERT: B 716 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7208 (tpm170) REVERT: C 145 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6897 (mp) REVERT: C 167 THR cc_start: 0.8051 (p) cc_final: 0.7667 (t) REVERT: C 253 LYS cc_start: 0.8223 (ttmp) cc_final: 0.7575 (mmtt) REVERT: C 327 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7128 (mmm160) REVERT: C 367 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7373 (pt0) REVERT: C 368 LYS cc_start: 0.8325 (mmmm) cc_final: 0.8121 (ttmt) REVERT: C 478 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6923 (tmmt) REVERT: C 702 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 712 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7664 (mtm110) REVERT: C 716 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7171 (tpp-160) REVERT: D 145 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7104 (mt) REVERT: D 148 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.6008 (mpt90) REVERT: D 202 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7932 (ptm160) REVERT: D 253 LYS cc_start: 0.8093 (ttmp) cc_final: 0.7633 (mptp) REVERT: D 291 SER cc_start: 0.8889 (m) cc_final: 0.8602 (p) REVERT: D 368 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8096 (ttmp) REVERT: D 431 MET cc_start: 0.7799 (mtp) cc_final: 0.6999 (mmt) REVERT: D 478 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6857 (tmmt) REVERT: D 482 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6603 (pt) REVERT: D 581 LYS cc_start: 0.7455 (tppt) cc_final: 0.6906 (mmpt) REVERT: D 641 ASP cc_start: 0.8494 (p0) cc_final: 0.8257 (p0) REVERT: D 690 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7822 (mtm110) REVERT: D 693 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8392 (mtt90) REVERT: D 702 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 716 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7246 (tpp-160) REVERT: D 741 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 85 outliers final: 24 residues processed: 398 average time/residue: 0.6409 time to fit residues: 292.3936 Evaluate side-chains 359 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 462 ARG Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 681 VAL 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 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 148 ARG 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 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 548 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121378 restraints weight = 26742.151| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.27 r_work: 0.3236 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23080 Z= 0.096 Angle : 0.517 7.819 30896 Z= 0.262 Chirality : 0.038 0.156 3308 Planarity : 0.004 0.055 3716 Dihedral : 19.565 140.162 4224 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.22 % Allowed : 17.20 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2552 helix: 1.44 (0.13), residues: 1636 sheet: -0.15 (0.44), residues: 112 loop : -2.13 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 188 TYR 0.017 0.001 TYR D 208 PHE 0.012 0.001 PHE C 316 TRP 0.012 0.001 TRP C 692 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (23076) covalent geometry : angle 0.51699 / 0.26 (30888) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.25805 / 0.17 ( 8) hydrogen bonds : bond 0.02836 / 1.84 ( 942) hydrogen bonds : angle 3.38608 / 2.28 ( 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 393 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 148 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.5358 (mpt180) REVERT: A 253 LYS cc_start: 0.8209 (ttmp) cc_final: 0.7715 (mmtt) REVERT: A 327 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7181 (mmm160) REVERT: A 478 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6962 (tmmt) REVERT: A 631 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: A 642 LEU cc_start: 0.8469 (mt) cc_final: 0.8232 (mt) REVERT: A 690 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7815 (mtm110) REVERT: A 702 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8366 (mm-30) REVERT: A 716 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7321 (tpm170) REVERT: A 717 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: B 159 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6359 (mmp) REVERT: B 202 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7685 (ptm160) REVERT: B 253 LYS cc_start: 0.8271 (ttmp) cc_final: 0.7676 (mmtt) REVERT: B 431 MET cc_start: 0.7878 (mtp) cc_final: 0.7608 (mtp) REVERT: B 478 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6979 (tmmt) REVERT: B 631 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: B 690 ARG cc_start: 0.8251 (mtt90) cc_final: 0.7848 (mtm110) REVERT: B 702 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 716 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7232 (tpm170) REVERT: C 167 THR cc_start: 0.8083 (p) cc_final: 0.7778 (t) REVERT: C 202 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7815 (ptm160) REVERT: C 253 LYS cc_start: 0.8235 (ttmp) cc_final: 0.7635 (mmtt) REVERT: C 327 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7194 (mmm160) REVERT: C 367 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7447 (pt0) REVERT: C 368 LYS cc_start: 0.8315 (mmmm) cc_final: 0.8089 (ttmt) REVERT: C 472 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7808 (Cg_endo) REVERT: C 478 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6797 (tmmt) REVERT: C 702 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8315 (mm-30) REVERT: C 712 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7650 (mtm110) REVERT: C 716 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7201 (tpp-160) REVERT: C 736 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: D 145 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7081 (mt) REVERT: D 202 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7934 (ptm160) REVERT: D 253 LYS cc_start: 0.8047 (ttmp) cc_final: 0.7651 (mmtt) REVERT: D 291 SER cc_start: 0.8893 (m) cc_final: 0.8626 (p) REVERT: D 368 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8087 (ttmp) REVERT: D 431 MET cc_start: 0.7837 (mtp) cc_final: 0.7073 (mmt) REVERT: D 478 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6743 (tmmt) REVERT: D 482 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6628 (pt) REVERT: D 581 LYS cc_start: 0.7570 (tppt) cc_final: 0.7289 (mmtm) REVERT: D 641 ASP cc_start: 0.8436 (p0) cc_final: 0.8221 (p0) REVERT: D 686 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7996 (mmtt) REVERT: D 690 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7815 (mtm110) REVERT: D 693 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8431 (mtt90) REVERT: D 702 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8366 (mm-30) REVERT: D 716 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7300 (tpp-160) outliers start: 73 outliers final: 26 residues processed: 372 average time/residue: 0.6520 time to fit residues: 278.4596 Evaluate side-chains 354 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 159 MET 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 484 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 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 681 VAL Chi-restraints excluded: chain C residue 712 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 165 SER 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 548 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 693 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 9 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 254 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119480 restraints weight = 26533.999| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.28 r_work: 0.3198 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23080 Z= 0.108 Angle : 0.541 6.536 30896 Z= 0.271 Chirality : 0.038 0.172 3308 Planarity : 0.004 0.055 3716 Dihedral : 19.296 134.862 4224 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.17 % Allowed : 17.64 % Favored : 79.19 % 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 are not related in a simple way. whole: 0.53 (0.17), residues: 2552 helix: 1.50 (0.13), residues: 1636 sheet: -0.14 (0.45), residues: 112 loop : -2.06 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 202 TYR 0.018 0.001 TYR D 208 PHE 0.012 0.001 PHE A 316 TRP 0.012 0.001 TRP C 710 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23076) covalent geometry : angle 0.54145 / 0.27 (30888) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.26403 / 0.17 ( 8) hydrogen bonds : bond 0.03046 / 1.97 ( 942) hydrogen bonds : angle 3.42735 / 2.31 ( 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 390 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 148 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5489 (mpt180) REVERT: A 202 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7608 (ptm160) REVERT: A 253 LYS cc_start: 0.8264 (ttmp) cc_final: 0.7768 (mmtt) REVERT: A 327 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7199 (mmm160) REVERT: A 368 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7821 (ttmt) REVERT: A 431 MET cc_start: 0.8045 (mtm) cc_final: 0.7192 (mmt) REVERT: A 478 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6967 (tmmt) REVERT: A 631 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 642 LEU cc_start: 0.8478 (mt) cc_final: 0.8276 (mt) REVERT: A 690 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7830 (mtm110) REVERT: A 716 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7261 (tpp-160) REVERT: B 159 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6603 (mmp) REVERT: B 253 LYS cc_start: 0.8266 (ttmp) cc_final: 0.7669 (mmtt) REVERT: B 368 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7707 (ttmt) REVERT: B 478 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6925 (tmmt) REVERT: B 631 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 690 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7781 (mtm110) REVERT: B 702 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 716 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7225 (tpm170) REVERT: C 167 THR cc_start: 0.8139 (p) cc_final: 0.7800 (t) REVERT: C 253 LYS cc_start: 0.8275 (ttmp) cc_final: 0.7677 (mmtt) REVERT: C 327 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7226 (mmm160) REVERT: C 367 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7438 (pt0) REVERT: C 368 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8076 (ttmt) REVERT: C 478 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6834 (tmmt) REVERT: C 641 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8024 (p0) REVERT: C 712 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7602 (mtm110) REVERT: C 716 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7238 (tpp-160) REVERT: C 736 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: C 741 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: D 202 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7918 (ptm160) REVERT: D 253 LYS cc_start: 0.8052 (ttmp) cc_final: 0.7652 (mmtt) REVERT: D 291 SER cc_start: 0.8890 (m) cc_final: 0.8638 (p) REVERT: D 368 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8086 (ttmp) REVERT: D 431 MET cc_start: 0.7880 (mtp) cc_final: 0.7148 (mmt) REVERT: D 478 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6763 (tmmt) REVERT: D 482 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6595 (pt) REVERT: D 581 LYS cc_start: 0.7542 (tppt) cc_final: 0.7270 (mmtm) REVERT: D 686 LYS cc_start: 0.8236 (mmtt) cc_final: 0.8025 (mmtt) REVERT: D 690 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7828 (mtm110) REVERT: D 693 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8438 (mtt90) REVERT: D 702 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8388 (mm-30) REVERT: D 716 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7301 (tpp-160) REVERT: D 741 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7410 (mp0) outliers start: 72 outliers final: 35 residues processed: 362 average time/residue: 0.6661 time to fit residues: 275.6704 Evaluate side-chains 361 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 323 MET 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 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 159 MET 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 484 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 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 641 ASP 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 741 GLU 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 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 203 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 229 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 228 optimal weight: 30.0000 chunk 184 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 643 ASN C 330 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119536 restraints weight = 26927.458| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.30 r_work: 0.3213 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.89 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: 33 | |-----------------------------------------------------------------------------| |-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: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23080 Z= 0.105 Angle : 0.537 7.683 30896 Z= 0.271 Chirality : 0.038 0.165 3308 Planarity : 0.004 0.055 3716 Dihedral : 18.873 115.347 4224 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.87 % Allowed : 18.43 % Favored : 78.70 % 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 are not related in a simple way. whole: 0.57 (0.17), residues: 2552 helix: 1.58 (0.13), residues: 1636 sheet: -0.05 (0.46), residues: 112 loop : -2.17 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 690 TYR 0.017 0.001 TYR D 208 PHE 0.012 0.001 PHE B 316 TRP 0.014 0.001 TRP C 710 HIS 0.010 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23076) covalent geometry : angle 0.53749 / 0.27 (30888) SS BOND : bond 0.00150 / 0.08 ( 4) SS BOND : angle 0.27918 / 0.19 ( 8) hydrogen bonds : bond 0.02953 / 1.91 ( 942) hydrogen bonds : angle 3.41601 / 2.30 ( 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 381 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6866 (mp) REVERT: A 148 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5526 (mpt180) REVERT: A 202 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7640 (ptm160) REVERT: A 253 LYS cc_start: 0.8282 (ttmp) cc_final: 0.7743 (mmtt) REVERT: A 327 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: A 368 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7838 (ttmt) REVERT: A 431 MET cc_start: 0.7885 (mtm) cc_final: 0.6990 (mmt) REVERT: A 478 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6843 (ttpt) REVERT: A 581 LYS cc_start: 0.8523 (tmtt) cc_final: 0.6891 (mmtm) REVERT: A 631 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 642 LEU cc_start: 0.8546 (mt) cc_final: 0.8297 (mt) REVERT: A 690 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7815 (mtm110) REVERT: A 702 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 716 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7309 (tpm170) REVERT: B 159 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6689 (mmp) REVERT: B 253 LYS cc_start: 0.8284 (ttmp) cc_final: 0.7688 (mmtt) REVERT: B 368 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7705 (ttmt) REVERT: B 478 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6915 (tmmt) REVERT: B 631 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 690 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7758 (mtm110) REVERT: B 702 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 716 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7242 (tpp-160) REVERT: C 167 THR cc_start: 0.8159 (p) cc_final: 0.7870 (t) REVERT: C 253 LYS cc_start: 0.8287 (ttmp) cc_final: 0.7682 (mmtt) REVERT: C 367 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7458 (pt0) REVERT: C 368 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8108 (ttmt) REVERT: C 461 TYR cc_start: 0.6812 (t80) cc_final: 0.6560 (t80) REVERT: C 478 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6867 (tmmt) REVERT: C 641 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7992 (p0) REVERT: C 687 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7846 (mm-30) REVERT: C 702 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8245 (mm-30) REVERT: C 712 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7607 (mtm110) REVERT: C 716 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7267 (tpp-160) REVERT: C 736 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: C 741 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: D 253 LYS cc_start: 0.8081 (ttmp) cc_final: 0.7668 (mmtt) REVERT: D 291 SER cc_start: 0.8879 (m) cc_final: 0.8638 (p) REVERT: D 368 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8144 (ttmt) REVERT: D 478 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6774 (tmmt) REVERT: D 482 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6620 (pt) REVERT: D 581 LYS cc_start: 0.7541 (tppt) cc_final: 0.7289 (mmtm) REVERT: D 686 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8033 (mmtt) REVERT: D 690 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7843 (mtm110) REVERT: D 693 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8442 (mtt90) REVERT: D 716 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7265 (tpp-160) REVERT: D 741 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7310 (mp0) outliers start: 65 outliers final: 31 residues processed: 358 average time/residue: 0.6567 time to fit residues: 269.1011 Evaluate side-chains 358 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 323 MET 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 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 159 MET 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 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP 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 641 ASP 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 741 GLU 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 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 186 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 643 ASN C 330 ASN C 643 ASN D 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121635 restraints weight = 26967.527| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.31 r_work: 0.3244 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 0.039 23080 Z= 0.094 Angle : 0.529 13.862 30896 Z= 0.266 Chirality : 0.038 0.158 3308 Planarity : 0.004 0.055 3716 Dihedral : 18.264 104.795 4224 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.12 % Allowed : 19.66 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2552 helix: 1.70 (0.13), residues: 1636 sheet: -0.01 (0.47), residues: 112 loop : -2.11 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 202 TYR 0.018 0.001 TYR C 540 PHE 0.012 0.001 PHE B 316 TRP 0.015 0.001 TRP D 710 HIS 0.009 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (23076) covalent geometry : angle 0.52951 / 0.27 (30888) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.27407 / 0.18 ( 8) hydrogen bonds : bond 0.02716 / 1.75 ( 942) hydrogen bonds : angle 3.37176 / 2.27 ( 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 360 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 148 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5543 (mpt180) REVERT: A 202 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.8033 (ptm160) REVERT: A 253 LYS cc_start: 0.8272 (ttmp) cc_final: 0.7768 (mmtt) REVERT: A 327 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7147 (mmm160) REVERT: A 431 MET cc_start: 0.7961 (mtm) cc_final: 0.7114 (mmp) REVERT: A 478 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6742 (ttpt) REVERT: A 631 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 642 LEU cc_start: 0.8487 (mt) cc_final: 0.8285 (mt) REVERT: A 690 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7785 (mtm110) REVERT: A 702 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 716 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7305 (tpp-160) REVERT: B 253 LYS cc_start: 0.8273 (ttmp) cc_final: 0.7725 (mmtt) REVERT: B 368 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7623 (ttmt) REVERT: B 478 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6859 (tmmt) REVERT: B 482 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6674 (pt) REVERT: B 631 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: B 690 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7786 (mtm110) REVERT: B 702 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 716 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7256 (tpm170) REVERT: C 167 THR cc_start: 0.8175 (p) cc_final: 0.7909 (t) REVERT: C 253 LYS cc_start: 0.8299 (ttmp) cc_final: 0.7727 (mmtt) REVERT: C 367 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7469 (pt0) REVERT: C 461 TYR cc_start: 0.6615 (t80) cc_final: 0.6368 (t80) REVERT: C 478 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6864 (tmmt) REVERT: C 482 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6547 (pt) REVERT: C 687 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7778 (mm-30) REVERT: C 702 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8268 (mm-30) REVERT: C 712 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7573 (mtm110) REVERT: C 716 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7275 (tpp-160) REVERT: D 253 LYS cc_start: 0.8062 (ttmp) cc_final: 0.7664 (mmtt) REVERT: D 291 SER cc_start: 0.8893 (m) cc_final: 0.8658 (p) REVERT: D 368 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8092 (ttmt) REVERT: D 431 MET cc_start: 0.8059 (mtm) cc_final: 0.7139 (mmt) REVERT: D 478 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6800 (tmmt) REVERT: D 482 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6551 (pt) REVERT: D 581 LYS cc_start: 0.7519 (tppt) cc_final: 0.7059 (mmpt) REVERT: D 686 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7982 (mmtt) REVERT: D 687 GLU cc_start: 0.8073 (tp30) cc_final: 0.7802 (tp30) REVERT: D 690 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7833 (mtm110) REVERT: D 702 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8320 (mm-30) REVERT: D 716 ARG cc_start: 0.8222 (ttp-170) cc_final: 0.7287 (tpp-160) REVERT: D 741 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7311 (mp0) outliers start: 48 outliers final: 21 residues processed: 346 average time/residue: 0.6378 time to fit residues: 252.5766 Evaluate side-chains 335 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 631 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 229 ASP 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 681 VAL Chi-restraints excluded: chain C residue 712 ARG 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 681 VAL Chi-restraints excluded: chain D residue 690 ARG Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.8980 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: 0.9990 chunk 132 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN B 643 ASN C 330 ASN 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 = 0.3971 r_free = 0.3971 target = 0.173128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121674 restraints weight = 26979.612| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.31 r_work: 0.3245 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23080 Z= 0.095 Angle : 0.524 9.755 30896 Z= 0.265 Chirality : 0.038 0.155 3308 Planarity : 0.004 0.055 3716 Dihedral : 17.937 102.069 4224 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.94 % Allowed : 20.06 % Favored : 78.00 % 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 are not related in a simple way. whole: 0.76 (0.17), residues: 2552 helix: 1.70 (0.13), residues: 1652 sheet: -0.03 (0.47), residues: 112 loop : -2.09 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 690 TYR 0.016 0.001 TYR D 208 PHE 0.012 0.001 PHE B 316 TRP 0.016 0.001 TRP C 710 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (23076) covalent geometry : angle 0.52409 / 0.27 (30888) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.28845 / 0.19 ( 8) hydrogen bonds : bond 0.02740 / 1.76 ( 942) hydrogen bonds : angle 3.35299 / 2.26 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9856.29 seconds wall clock time: 168 minutes 31.22 seconds (10111.22 seconds total)