Starting phenix.real_space_refine on Sun Sep 13 16:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pw5_20499/09_2026/6pw5_20499.map" } resolution = 3.45 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 190 5.16 5 C 15986 2.51 5 N 4036 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5858 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 3 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6197 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5858 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 3 Chain: "D" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6197 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.34, per 1000 atoms: 0.22 Number of scatterers: 24740 At special positions: 0 Unit cell: (159.6, 160.55, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 190 16.00 P 28 15.00 O 4500 8.00 N 4036 7.00 C 15986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 668 " - pdb=" SG CYS A 678 " distance=2.03 Simple disulfide: pdb=" SG CYS B 668 " - pdb=" SG CYS B 678 " distance=2.03 Simple disulfide: pdb=" SG CYS C 668 " - pdb=" SG CYS C 678 " distance=2.04 Simple disulfide: pdb=" SG CYS D 668 " - pdb=" SG CYS D 678 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 985.3 milliseconds 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 0 sheets defined 65.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.690A pdb=" N VAL A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.927A pdb=" N ALA A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.564A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.776A pdb=" N TYR A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.708A pdb=" N GLU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 4.092A pdb=" N LEU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 333 through 347 removed outlier: 3.544A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.510A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 removed outlier: 3.830A pdb=" N ALA A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.670A pdb=" N ILE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.558A pdb=" N THR A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.606A pdb=" N ILE A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 3.560A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.001A pdb=" N GLN A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 Processing helix chain 'A' and resid 497 through 522 removed outlier: 4.049A pdb=" N PHE A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.755A pdb=" N ALA A 531 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 532 " --> pdb=" O VAL A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 532' Processing helix chain 'A' and resid 538 through 556 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.795A pdb=" N THR A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 579 " --> pdb=" O MET A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 3.601A pdb=" N ASN A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.721A pdb=" N ILE A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 665 removed outlier: 3.684A pdb=" N VAL A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 751 removed outlier: 3.857A pdb=" N GLY A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.517A pdb=" N GLU A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 763 " --> pdb=" O ARG A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 797 removed outlier: 3.502A pdb=" N HIS A 783 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 849 removed outlier: 3.685A pdb=" N ASN A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 856 Processing helix chain 'A' and resid 857 through 869 removed outlier: 4.093A pdb=" N HIS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.610A pdb=" N GLN B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.655A pdb=" N LEU B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.616A pdb=" N LEU B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.296A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.684A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 removed outlier: 4.099A pdb=" N VAL B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 removed outlier: 3.748A pdb=" N THR B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.736A pdb=" N SER B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 368 through 386 removed outlier: 3.694A pdb=" N VAL B 372 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.684A pdb=" N LEU B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.756A pdb=" N ILE B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.781A pdb=" N LYS B 442 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 443 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 461 removed outlier: 3.574A pdb=" N LEU B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 removed outlier: 3.978A pdb=" N SER B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.687A pdb=" N GLN B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 520 removed outlier: 3.745A pdb=" N THR B 511 " --> pdb=" O CYS B 507 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 534 through 557 removed outlier: 3.699A pdb=" N ALA B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 548 " --> pdb=" O CYS B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.838A pdb=" N SER B 566 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.609A pdb=" N VAL B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 615 removed outlier: 3.737A pdb=" N LEU B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 4.022A pdb=" N VAL B 620 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 622 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 623 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.515A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 removed outlier: 4.834A pdb=" N LEU B 647 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 753 removed outlier: 3.763A pdb=" N THR B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY B 720 " --> pdb=" O LYS B 716 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 723 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 734 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.511A pdb=" N ALA B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 removed outlier: 4.713A pdb=" N LEU B 781 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 783 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 791 removed outlier: 3.727A pdb=" N ASN B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 4.369A pdb=" N VAL B 797 " --> pdb=" O LEU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 842 removed outlier: 3.535A pdb=" N VAL B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 840 " --> pdb=" O ARG B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 removed outlier: 3.870A pdb=" N ALA B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 872 removed outlier: 3.622A pdb=" N LEU B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS B 869 " --> pdb=" O MET B 865 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 870 " --> pdb=" O LEU B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.665A pdb=" N VAL C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.929A pdb=" N ALA C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.563A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 152 removed outlier: 3.780A pdb=" N TYR C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.709A pdb=" N GLU C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 220 removed outlier: 4.092A pdb=" N LEU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 333 through 347 removed outlier: 3.544A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.510A pdb=" N LEU C 362 " --> pdb=" O CYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 377 removed outlier: 3.829A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.673A pdb=" N ILE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 423 through 433 removed outlier: 3.563A pdb=" N THR C 429 " --> pdb=" O GLN C 425 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 443 through 460 Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.610A pdb=" N ILE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Proline residue: C 466 - end of helix removed outlier: 3.570A pdb=" N ALA C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.999A pdb=" N GLN C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 496 Processing helix chain 'C' and resid 497 through 522 removed outlier: 4.033A pdb=" N PHE C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.761A pdb=" N ALA C 531 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 532 " --> pdb=" O VAL C 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 528 through 532' Processing helix chain 'C' and resid 538 through 556 Processing helix chain 'C' and resid 559 through 565 Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.794A pdb=" N THR C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR C 579 " --> pdb=" O MET C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 removed outlier: 3.602A pdb=" N ASN C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.512A pdb=" N GLN C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET C 633 " --> pdb=" O PRO C 629 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 665 removed outlier: 3.686A pdb=" N VAL C 651 " --> pdb=" O LEU C 647 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 751 removed outlier: 3.855A pdb=" N GLY C 720 " --> pdb=" O LYS C 716 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 741 " --> pdb=" O ASN C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 767 removed outlier: 4.706A pdb=" N ARG C 759 " --> pdb=" O MET C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 797 removed outlier: 3.502A pdb=" N HIS C 783 " --> pdb=" O PHE C 779 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 784 " --> pdb=" O ASN C 780 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG C 794 " --> pdb=" O GLY C 790 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 796 " --> pdb=" O GLY C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 849 removed outlier: 3.686A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 856 Processing helix chain 'C' and resid 857 through 869 removed outlier: 4.090A pdb=" N HIS C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 27 removed outlier: 3.610A pdb=" N GLN D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.655A pdb=" N LEU D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.616A pdb=" N LEU D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 139 through 153 removed outlier: 4.296A pdb=" N TYR D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.684A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 removed outlier: 4.100A pdb=" N VAL D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 removed outlier: 3.748A pdb=" N THR D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 250 through 256 Processing helix chain 'D' and resid 333 through 346 removed outlier: 3.736A pdb=" N SER D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 368 through 386 removed outlier: 3.694A pdb=" N VAL D 372 " --> pdb=" O PHE D 368 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.682A pdb=" N LEU D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.756A pdb=" N ILE D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 428 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 429 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.783A pdb=" N LYS D 442 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D 443 " --> pdb=" O TYR D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.574A pdb=" N LEU D 454 " --> pdb=" O GLY D 450 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 475 removed outlier: 3.984A pdb=" N SER D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.660A pdb=" N GLN D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 520 removed outlier: 3.744A pdb=" N THR D 511 " --> pdb=" O CYS D 507 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 534 through 557 removed outlier: 3.699A pdb=" N ALA D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 548 " --> pdb=" O CYS D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 removed outlier: 3.837A pdb=" N SER D 566 " --> pdb=" O TYR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 592 removed outlier: 3.609A pdb=" N VAL D 573 " --> pdb=" O ASN D 569 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 584 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 615 removed outlier: 3.736A pdb=" N LEU D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 607 " --> pdb=" O ASN D 603 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 613 " --> pdb=" O ALA D 609 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 623 removed outlier: 4.041A pdb=" N VAL D 620 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 622 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 623 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.533A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 637 " --> pdb=" O MET D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 4.839A pdb=" N LEU D 647 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 648 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 651 " --> pdb=" O LEU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 720 removed outlier: 3.750A pdb=" N THR D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 720 " --> pdb=" O LYS D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 715 through 720' Processing helix chain 'D' and resid 720 through 753 removed outlier: 3.532A pdb=" N ILE D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 734 " --> pdb=" O VAL D 730 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D 745 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 767 removed outlier: 3.511A pdb=" N ALA D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 785 removed outlier: 4.714A pdb=" N LEU D 781 " --> pdb=" O PRO D 777 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU D 782 " --> pdb=" O PRO D 778 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 783 " --> pdb=" O PHE D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 791 removed outlier: 3.709A pdb=" N ASN D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 4.401A pdb=" N VAL D 797 " --> pdb=" O LEU D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 842 removed outlier: 3.534A pdb=" N VAL D 832 " --> pdb=" O ARG D 828 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 857 removed outlier: 3.860A pdb=" N ALA D 848 " --> pdb=" O SER D 844 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 852 " --> pdb=" O ALA D 848 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 856 " --> pdb=" O GLU D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 872 removed outlier: 3.620A pdb=" N LEU D 861 " --> pdb=" O GLU D 857 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D 868 " --> pdb=" O GLU D 864 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS D 869 " --> pdb=" O MET D 865 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 870 " --> pdb=" O LEU D 866 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3234 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: 3.95 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3898 1.30 - 1.43: 6803 1.43 - 1.57: 14229 1.57 - 1.70: 42 1.70 - 1.83: 308 Bond restraints: 25280 Sorted by residual: bond pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 1.332 1.408 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1A PIO A1001 " pdb=" O2C PIO A1001 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" CB1 PIK C1003 " pdb=" OB1 PIK C1003 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB1 PIK A1003 " pdb=" OB1 PIK A1003 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C11 PCW B1002 " pdb=" O3 PCW B1002 " ideal model delta sigma weight residual 1.326 1.398 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 25275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 33063 3.64 - 7.27: 1017 7.27 - 10.91: 159 10.91 - 14.54: 26 14.54 - 18.18: 5 Bond angle restraints: 34270 Sorted by residual: angle pdb=" N VAL A 380 " pdb=" CA VAL A 380 " pdb=" C VAL A 380 " ideal model delta sigma weight residual 113.42 105.89 7.53 1.17e+00 7.31e-01 4.15e+01 angle pdb=" N VAL C 380 " pdb=" CA VAL C 380 " pdb=" C VAL C 380 " ideal model delta sigma weight residual 113.42 105.89 7.53 1.17e+00 7.31e-01 4.15e+01 angle pdb=" C GLY A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C GLY C 75 " pdb=" N GLN C 76 " pdb=" CA GLN C 76 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" N SER B 683 " pdb=" CA SER B 683 " pdb=" C SER B 683 " ideal model delta sigma weight residual 112.12 119.81 -7.69 1.34e+00 5.57e-01 3.29e+01 ... (remaining 34265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 14623 33.52 - 67.04: 329 67.04 - 100.56: 32 100.56 - 134.08: 4 134.08 - 167.60: 8 Dihedral angle restraints: 14996 sinusoidal: 6110 harmonic: 8886 Sorted by residual: dihedral pdb=" CA PRO B 272 " pdb=" C PRO B 272 " pdb=" N THR B 273 " pdb=" CA THR B 273 " ideal model delta harmonic sigma weight residual -180.00 -110.03 -69.97 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA PRO D 272 " pdb=" C PRO D 272 " pdb=" N THR D 273 " pdb=" CA THR D 273 " ideal model delta harmonic sigma weight residual -180.00 -112.98 -67.02 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA ARG B 231 " pdb=" C ARG B 231 " pdb=" N SER B 232 " pdb=" CA SER B 232 " ideal model delta harmonic sigma weight residual -180.00 -130.03 -49.97 0 5.00e+00 4.00e-02 9.99e+01 ... (remaining 14993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3416 0.095 - 0.191: 416 0.191 - 0.286: 46 0.286 - 0.381: 9 0.381 - 0.476: 1 Chirality restraints: 3888 Sorted by residual: chirality pdb=" CB VAL C 618 " pdb=" CA VAL C 618 " pdb=" CG1 VAL C 618 " pdb=" CG2 VAL C 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CB VAL A 618 " pdb=" CA VAL A 618 " pdb=" CG1 VAL A 618 " pdb=" CG2 VAL A 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C2 PCW A1002 " pdb=" C1 PCW A1002 " pdb=" C3 PCW A1002 " pdb=" O2 PCW A1002 " both_signs ideal model delta sigma weight residual False -2.32 -1.98 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 3885 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 231 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ARG D 231 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG D 231 " 0.029 2.00e-02 2.50e+03 pdb=" N SER D 232 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 231 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG B 231 " -0.078 2.00e-02 2.50e+03 pdb=" O ARG B 231 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 232 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 543 " 0.028 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP C 543 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 543 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 543 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 543 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 543 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 543 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 543 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 543 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 543 " 0.002 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8161 2.84 - 3.36: 22343 3.36 - 3.87: 38647 3.87 - 4.39: 47478 4.39 - 4.90: 78969 Nonbonded interactions: 195598 Sorted by model distance: nonbonded pdb=" NH1 ARG C 501 " pdb=" O TYR C 769 " model vdw 2.327 3.120 nonbonded pdb=" NH1 ARG A 501 " pdb=" O TYR A 769 " model vdw 2.328 3.120 nonbonded pdb=" O ILE C 78 " pdb=" OG SER C 89 " model vdw 2.346 3.040 nonbonded pdb=" NE1 TRP D 568 " pdb=" OE2 GLU D 622 " model vdw 2.351 3.120 nonbonded pdb=" NE1 TRP B 568 " pdb=" OE2 GLU B 622 " model vdw 2.351 3.120 ... (remaining 195593 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.013 0.095 25288 Z= 0.545 Angle : 1.495 18.180 34278 Z= 0.715 Chirality : 0.068 0.476 3888 Planarity : 0.009 0.082 4220 Dihedral : 14.736 167.604 9236 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.77 % Allowed : 11.62 % Favored : 87.62 % Rotamer: Outliers : 1.61 % Allowed : 6.73 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.62 % 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: -6.95 (0.09), residues: 3004 helix: -4.65 (0.05), residues: 1920 sheet: None (None), residues: 0 loop : -4.17 (0.14), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 761 TYR 0.045 0.005 TYR D 820 PHE 0.034 0.004 PHE D 233 TRP 0.064 0.005 TRP C 543 HIS 0.034 0.005 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.01301 / 0.55 (25280) covalent geometry : angle 1.49495 / 0.71 (34270) SS BOND : bond 0.00294 / 0.15 ( 4) SS BOND : angle 2.05238 / 0.99 ( 8) hydrogen bonds : bond 0.33224 / 21.70 ( 1096) hydrogen bonds : angle 10.77050 / 7.31 ( 3234) Misc. bond : bond 0.00319 / 0.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 548 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.9252 (mtt) cc_final: 0.9052 (mtm) REVERT: A 475 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7789 (tm) REVERT: A 518 TYR cc_start: 0.8653 (t80) cc_final: 0.8439 (t80) REVERT: A 564 MET cc_start: 0.7006 (mmm) cc_final: 0.6452 (mtp) REVERT: A 630 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9099 (tp) REVERT: A 636 GLN cc_start: 0.8162 (tt0) cc_final: 0.7934 (tt0) REVERT: A 814 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 57 ILE cc_start: 0.9038 (tt) cc_final: 0.8801 (mt) REVERT: B 180 THR cc_start: 0.9388 (m) cc_final: 0.9154 (p) REVERT: B 439 ASP cc_start: 0.7942 (t70) cc_final: 0.7126 (t0) REVERT: B 580 ILE cc_start: 0.9132 (tp) cc_final: 0.8813 (mt) REVERT: B 661 GLU cc_start: 0.7510 (tp30) cc_final: 0.7236 (tp30) REVERT: B 733 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8614 (mt) REVERT: C 67 LYS cc_start: 0.8893 (tptt) cc_final: 0.8690 (tppt) REVERT: C 475 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7774 (tm) REVERT: C 518 TYR cc_start: 0.8653 (t80) cc_final: 0.8437 (t80) REVERT: C 564 MET cc_start: 0.6905 (mmm) cc_final: 0.6583 (mtp) REVERT: C 814 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7911 (m) REVERT: D 57 ILE cc_start: 0.9036 (tt) cc_final: 0.8797 (mt) REVERT: D 180 THR cc_start: 0.9426 (m) cc_final: 0.9165 (p) REVERT: D 439 ASP cc_start: 0.7937 (t70) cc_final: 0.7133 (t0) REVERT: D 580 ILE cc_start: 0.9127 (tp) cc_final: 0.8812 (mt) REVERT: D 661 GLU cc_start: 0.7507 (tp30) cc_final: 0.7240 (tp30) REVERT: D 733 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8588 (mt) REVERT: D 759 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8362 (mtm180) outliers start: 42 outliers final: 11 residues processed: 578 average time/residue: 0.1918 time to fit residues: 169.6238 Evaluate side-chains 376 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 358 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 733 ILE Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 HIS A 97 ASN A 177 GLN A 179 HIS A 364 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 636 GLN B 120 HIS B 152 GLN B 177 GLN B 179 HIS B 479 GLN B 506 GLN B 665 GLN B 676 ASN B 737 ASN B 860 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 97 ASN C 177 GLN C 179 HIS C 364 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 120 HIS D 152 GLN D 177 GLN D 179 HIS D 479 GLN D 506 GLN D 665 GLN D 676 ASN D 737 ASN D 860 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.156610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117289 restraints weight = 30552.299| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.83 r_work: 0.2994 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25288 Z= 0.128 Angle : 0.674 9.488 34278 Z= 0.347 Chirality : 0.040 0.187 3888 Planarity : 0.006 0.068 4220 Dihedral : 13.127 170.833 3654 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.59 % Favored : 90.08 % Rotamer: Outliers : 3.56 % Allowed : 10.71 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.53 (0.12), residues: 3004 helix: -2.56 (0.09), residues: 1942 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 828 TYR 0.018 0.001 TYR A 583 PHE 0.014 0.001 PHE B 803 TRP 0.017 0.001 TRP D 543 HIS 0.011 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (25280) covalent geometry : angle 0.67347 / 0.35 (34270) SS BOND : bond 0.00049 / 0.03 ( 4) SS BOND : angle 0.84549 / 0.41 ( 8) hydrogen bonds : bond 0.04074 / 2.72 ( 1096) hydrogen bonds : angle 4.72278 / 3.23 ( 3234) Misc. bond : bond 0.00024 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 500 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8469 (tppt) cc_final: 0.8196 (mmtp) REVERT: A 489 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 564 MET cc_start: 0.6736 (mmm) cc_final: 0.5712 (mtp) REVERT: A 737 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8888 (t0) REVERT: B 32 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6815 (ptm-80) REVERT: B 57 ILE cc_start: 0.9018 (tt) cc_final: 0.8715 (mt) REVERT: B 71 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 85 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7257 (p90) REVERT: B 103 GLN cc_start: 0.8772 (tt0) cc_final: 0.8396 (tt0) REVERT: B 214 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8810 (tt) REVERT: B 439 ASP cc_start: 0.8381 (t70) cc_final: 0.7529 (t0) REVERT: B 483 MET cc_start: 0.7398 (mmm) cc_final: 0.6648 (tmm) REVERT: B 555 TYR cc_start: 0.8317 (t80) cc_final: 0.7830 (t80) REVERT: B 581 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8786 (mt) REVERT: B 661 GLU cc_start: 0.8188 (tp30) cc_final: 0.7761 (tp30) REVERT: B 733 ILE cc_start: 0.8927 (mp) cc_final: 0.8609 (mt) REVERT: C 67 LYS cc_start: 0.8601 (tptt) cc_final: 0.8233 (tppt) REVERT: C 489 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7836 (p) REVERT: C 564 MET cc_start: 0.6671 (mmm) cc_final: 0.5699 (mtp) REVERT: C 636 GLN cc_start: 0.8149 (tt0) cc_final: 0.7752 (mt0) REVERT: C 737 ASN cc_start: 0.9212 (OUTLIER) cc_final: 0.8850 (t0) REVERT: D 32 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6777 (ptm-80) REVERT: D 57 ILE cc_start: 0.9031 (tt) cc_final: 0.8742 (mt) REVERT: D 71 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 85 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7279 (p90) REVERT: D 103 GLN cc_start: 0.8754 (tt0) cc_final: 0.8374 (tt0) REVERT: D 150 ASP cc_start: 0.8301 (m-30) cc_final: 0.8097 (m-30) REVERT: D 214 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (tt) REVERT: D 439 ASP cc_start: 0.8403 (t70) cc_final: 0.7545 (t0) REVERT: D 483 MET cc_start: 0.7381 (mmm) cc_final: 0.6618 (tmm) REVERT: D 555 TYR cc_start: 0.8309 (t80) cc_final: 0.7819 (t80) REVERT: D 581 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8786 (mt) REVERT: D 661 GLU cc_start: 0.8205 (tp30) cc_final: 0.7763 (tp30) REVERT: D 733 ILE cc_start: 0.8904 (mp) cc_final: 0.8583 (mt) outliers start: 93 outliers final: 34 residues processed: 555 average time/residue: 0.1504 time to fit residues: 135.0933 Evaluate side-chains 419 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 674 THR Chi-restraints excluded: chain C residue 737 ASN Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 59 optimal weight: 6.9990 chunk 172 optimal weight: 0.0070 chunk 211 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 ASN B 76 GLN B 569 ASN B 632 GLN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 569 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.157069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119549 restraints weight = 30765.799| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.2968 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25288 Z= 0.112 Angle : 0.609 7.925 34278 Z= 0.313 Chirality : 0.039 0.167 3888 Planarity : 0.005 0.070 4220 Dihedral : 11.153 170.334 3638 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.59 % Favored : 90.01 % Rotamer: Outliers : 3.79 % Allowed : 13.12 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.90 (0.14), residues: 3004 helix: -1.14 (0.11), residues: 1966 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 828 TYR 0.027 0.001 TYR C 518 PHE 0.011 0.001 PHE A 841 TRP 0.019 0.001 TRP C 798 HIS 0.008 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25280) covalent geometry : angle 0.60886 / 0.31 (34270) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.78796 / 0.38 ( 8) hydrogen bonds : bond 0.03387 / 2.26 ( 1096) hydrogen bonds : angle 3.98508 / 2.72 ( 3234) Misc. bond : bond 0.00032 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 397 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7386 (mmm160) REVERT: A 489 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (p) REVERT: A 564 MET cc_start: 0.6514 (mmm) cc_final: 0.5651 (mtp) REVERT: A 569 ASN cc_start: 0.7920 (m110) cc_final: 0.7657 (p0) REVERT: A 636 GLN cc_start: 0.8024 (tt0) cc_final: 0.7798 (mt0) REVERT: B 32 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6987 (ptm-80) REVERT: B 62 LEU cc_start: 0.9441 (mm) cc_final: 0.9224 (mp) REVERT: B 435 MET cc_start: 0.9022 (tpp) cc_final: 0.8773 (mmp) REVERT: B 439 ASP cc_start: 0.8152 (t70) cc_final: 0.7332 (t0) REVERT: B 581 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8782 (mt) REVERT: B 661 GLU cc_start: 0.7895 (tp30) cc_final: 0.7482 (tp30) REVERT: B 664 PHE cc_start: 0.8111 (m-10) cc_final: 0.7900 (m-10) REVERT: B 733 ILE cc_start: 0.8895 (mp) cc_final: 0.8507 (mt) REVERT: C 67 LYS cc_start: 0.8562 (tptt) cc_final: 0.8223 (tppt) REVERT: C 223 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7171 (mmm160) REVERT: C 411 LEU cc_start: 0.8851 (pp) cc_final: 0.8544 (pt) REVERT: C 489 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7801 (p) REVERT: C 564 MET cc_start: 0.6531 (mmm) cc_final: 0.5697 (mtp) REVERT: C 569 ASN cc_start: 0.8072 (m-40) cc_final: 0.7697 (p0) REVERT: C 636 GLN cc_start: 0.8044 (tt0) cc_final: 0.7761 (mt0) REVERT: D 32 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6939 (ptm-80) REVERT: D 62 LEU cc_start: 0.9440 (mm) cc_final: 0.9229 (mp) REVERT: D 439 ASP cc_start: 0.8158 (t70) cc_final: 0.7357 (t0) REVERT: D 581 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8776 (mt) REVERT: D 661 GLU cc_start: 0.7879 (tp30) cc_final: 0.7248 (tp30) REVERT: D 664 PHE cc_start: 0.8129 (m-10) cc_final: 0.7920 (m-10) REVERT: D 733 ILE cc_start: 0.8831 (mp) cc_final: 0.8381 (mt) outliers start: 99 outliers final: 47 residues processed: 456 average time/residue: 0.1613 time to fit residues: 119.0144 Evaluate side-chains 394 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 261 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN B 86 HIS B 152 GLN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN B 863 HIS ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN C 569 ASN C 636 GLN D 152 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN D 863 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107028 restraints weight = 30638.401| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.97 r_work: 0.2881 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25288 Z= 0.214 Angle : 0.706 8.933 34278 Z= 0.356 Chirality : 0.043 0.173 3888 Planarity : 0.005 0.070 4220 Dihedral : 11.023 167.028 3638 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.25 % Favored : 90.35 % Rotamer: Outliers : 4.06 % Allowed : 14.15 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.46 (0.15), residues: 3004 helix: -0.73 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -3.40 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 828 TYR 0.028 0.002 TYR A 747 PHE 0.019 0.002 PHE D 234 TRP 0.020 0.002 TRP D 543 HIS 0.010 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (25280) covalent geometry : angle 0.70640 / 0.36 (34270) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 0.62409 / 0.30 ( 8) hydrogen bonds : bond 0.04064 / 2.71 ( 1096) hydrogen bonds : angle 4.10243 / 2.80 ( 3234) Misc. bond : bond 0.00093 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 354 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (mmm160) REVERT: A 489 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7961 (p) REVERT: A 564 MET cc_start: 0.6606 (mmm) cc_final: 0.5670 (mtp) REVERT: A 636 GLN cc_start: 0.8354 (tt0) cc_final: 0.8066 (mt0) REVERT: B 32 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6915 (ptm-80) REVERT: B 187 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 558 GLU cc_start: 0.6456 (pt0) cc_final: 0.6241 (pt0) REVERT: B 581 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 661 GLU cc_start: 0.7990 (tp30) cc_final: 0.7694 (tp30) REVERT: B 664 PHE cc_start: 0.8424 (m-10) cc_final: 0.8144 (m-10) REVERT: B 733 ILE cc_start: 0.8913 (mp) cc_final: 0.8631 (mt) REVERT: C 67 LYS cc_start: 0.8568 (tptt) cc_final: 0.8216 (tppt) REVERT: C 489 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7952 (p) REVERT: C 564 MET cc_start: 0.6606 (mmm) cc_final: 0.5713 (mtp) REVERT: C 569 ASN cc_start: 0.8340 (m110) cc_final: 0.7951 (p0) REVERT: C 636 GLN cc_start: 0.8376 (tt0) cc_final: 0.8144 (mt0) REVERT: C 794 ARG cc_start: 0.5761 (mtt90) cc_final: 0.5006 (ttp80) REVERT: D 32 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6887 (ptm-80) REVERT: D 123 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6089 (tpt170) REVERT: D 187 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8569 (tt) REVERT: D 492 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7215 (mtm180) REVERT: D 558 GLU cc_start: 0.6421 (pt0) cc_final: 0.6204 (pt0) REVERT: D 581 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (mt) REVERT: D 661 GLU cc_start: 0.8057 (tp30) cc_final: 0.7775 (tp30) REVERT: D 664 PHE cc_start: 0.8417 (m-10) cc_final: 0.8063 (m-10) REVERT: D 733 ILE cc_start: 0.8925 (mp) cc_final: 0.8631 (mt) outliers start: 106 outliers final: 65 residues processed: 420 average time/residue: 0.1532 time to fit residues: 104.0444 Evaluate side-chains 407 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 730 VAL Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 300 optimal weight: 0.9980 chunk 296 optimal weight: 0.0970 chunk 75 optimal weight: 0.0980 chunk 168 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN C 843 ASN D 632 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.156508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114785 restraints weight = 30574.061| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.95 r_work: 0.2973 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25288 Z= 0.108 Angle : 0.588 7.445 34278 Z= 0.302 Chirality : 0.038 0.160 3888 Planarity : 0.005 0.072 4220 Dihedral : 10.056 168.244 3634 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.89 % Favored : 90.71 % Rotamer: Outliers : 3.52 % Allowed : 15.23 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.76 (0.15), residues: 3004 helix: -0.13 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.28 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 828 TYR 0.022 0.001 TYR A 747 PHE 0.012 0.001 PHE A 841 TRP 0.010 0.001 TRP D 684 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (25280) covalent geometry : angle 0.58780 / 0.30 (34270) SS BOND : bond 0.00080 / 0.04 ( 4) SS BOND : angle 0.37403 / 0.18 ( 8) hydrogen bonds : bond 0.02867 / 1.92 ( 1096) hydrogen bonds : angle 3.70146 / 2.54 ( 3234) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 373 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7318 (mmm160) REVERT: A 564 MET cc_start: 0.6481 (mmm) cc_final: 0.5480 (mtp) REVERT: A 569 ASN cc_start: 0.8101 (m110) cc_final: 0.7683 (p0) REVERT: A 582 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.8410 (t70) REVERT: A 636 GLN cc_start: 0.8299 (tt0) cc_final: 0.8019 (mt0) REVERT: A 794 ARG cc_start: 0.5189 (mtt90) cc_final: 0.4587 (ttp80) REVERT: A 812 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 483 MET cc_start: 0.6718 (mmm) cc_final: 0.6256 (tpp) REVERT: B 581 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8802 (mt) REVERT: B 661 GLU cc_start: 0.7909 (tp30) cc_final: 0.7579 (tp30) REVERT: B 664 PHE cc_start: 0.8280 (m-10) cc_final: 0.8055 (m-10) REVERT: B 733 ILE cc_start: 0.8877 (mp) cc_final: 0.8470 (mt) REVERT: C 67 LYS cc_start: 0.8513 (tptt) cc_final: 0.8170 (mmtp) REVERT: C 223 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7231 (mmm160) REVERT: C 411 LEU cc_start: 0.8961 (pp) cc_final: 0.8572 (pt) REVERT: C 564 MET cc_start: 0.6568 (mmm) cc_final: 0.5588 (mtp) REVERT: C 582 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8414 (t70) REVERT: C 636 GLN cc_start: 0.8248 (tt0) cc_final: 0.7892 (mt0) REVERT: C 794 ARG cc_start: 0.5396 (mtt90) cc_final: 0.4939 (ttp-170) REVERT: C 812 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6870 (mt-10) REVERT: D 123 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.3888 (ttp80) REVERT: D 492 ARG cc_start: 0.7281 (mtm180) cc_final: 0.7075 (mtm180) REVERT: D 581 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8809 (mt) REVERT: D 661 GLU cc_start: 0.7947 (tp30) cc_final: 0.7622 (tp30) REVERT: D 664 PHE cc_start: 0.8263 (m-10) cc_final: 0.8035 (m-10) REVERT: D 733 ILE cc_start: 0.8856 (mp) cc_final: 0.8595 (mt) outliers start: 92 outliers final: 52 residues processed: 431 average time/residue: 0.1495 time to fit residues: 106.7509 Evaluate side-chains 403 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 344 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 865 MET Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 808 MET Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 191 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 737 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 ASN D 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.150294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108998 restraints weight = 30839.000| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.89 r_work: 0.2889 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25288 Z= 0.198 Angle : 0.677 13.079 34278 Z= 0.339 Chirality : 0.042 0.173 3888 Planarity : 0.005 0.073 4220 Dihedral : 10.265 169.184 3634 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.29 % Favored : 90.31 % Rotamer: Outliers : 3.06 % Allowed : 16.53 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.70 (0.15), residues: 3004 helix: -0.08 (0.12), residues: 1986 sheet: None (None), residues: 0 loop : -3.27 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 828 TYR 0.023 0.002 TYR C 747 PHE 0.016 0.001 PHE A 723 TRP 0.020 0.002 TRP A 432 HIS 0.007 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (25280) covalent geometry : angle 0.67665 / 0.34 (34270) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.53084 / 0.26 ( 8) hydrogen bonds : bond 0.03703 / 2.48 ( 1096) hydrogen bonds : angle 3.89628 / 2.66 ( 3234) Misc. bond : bond 0.00094 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 339 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8418 (tppt) cc_final: 0.8193 (mmtp) REVERT: A 223 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7263 (mmm160) REVERT: A 326 LYS cc_start: 0.8567 (mttp) cc_final: 0.7981 (mtmm) REVERT: A 564 MET cc_start: 0.6575 (mmm) cc_final: 0.5605 (mtp) REVERT: A 571 MET cc_start: 0.8524 (ttm) cc_final: 0.8291 (tpp) REVERT: A 582 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8574 (t70) REVERT: A 636 GLN cc_start: 0.8339 (tt0) cc_final: 0.8068 (mt0) REVERT: A 794 ARG cc_start: 0.5257 (mtt90) cc_final: 0.4602 (ttp80) REVERT: B 483 MET cc_start: 0.6773 (mmm) cc_final: 0.6530 (tpp) REVERT: B 664 PHE cc_start: 0.8444 (m-10) cc_final: 0.8035 (m-10) REVERT: B 733 ILE cc_start: 0.8868 (mp) cc_final: 0.8614 (mt) REVERT: C 67 LYS cc_start: 0.8544 (tptt) cc_final: 0.8239 (mmtp) REVERT: C 223 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7262 (mmm160) REVERT: C 326 LYS cc_start: 0.8573 (mttp) cc_final: 0.7981 (mtmm) REVERT: C 564 MET cc_start: 0.6567 (mmm) cc_final: 0.5665 (mtp) REVERT: C 569 ASN cc_start: 0.8344 (m110) cc_final: 0.7796 (p0) REVERT: C 571 MET cc_start: 0.8531 (ttm) cc_final: 0.8312 (tpp) REVERT: C 582 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8538 (t70) REVERT: C 794 ARG cc_start: 0.5503 (mtt90) cc_final: 0.4843 (ttp80) REVERT: C 812 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6604 (pp20) REVERT: D 123 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6077 (tpt170) REVERT: D 483 MET cc_start: 0.6444 (tpp) cc_final: 0.6235 (tpp) REVERT: D 664 PHE cc_start: 0.8443 (m-10) cc_final: 0.8039 (m-10) REVERT: D 733 ILE cc_start: 0.8899 (mp) cc_final: 0.8621 (mt) outliers start: 80 outliers final: 61 residues processed: 396 average time/residue: 0.1505 time to fit residues: 98.6520 Evaluate side-chains 387 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 44 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 186 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.158102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.117181 restraints weight = 30082.072| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.92 r_work: 0.2922 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25288 Z= 0.135 Angle : 0.621 13.946 34278 Z= 0.313 Chirality : 0.040 0.165 3888 Planarity : 0.005 0.075 4220 Dihedral : 9.911 169.817 3634 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.15 % Favored : 90.45 % Rotamer: Outliers : 3.18 % Allowed : 16.83 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.41 (0.16), residues: 3004 helix: 0.15 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 828 TYR 0.020 0.001 TYR C 747 PHE 0.010 0.001 PHE D 803 TRP 0.014 0.001 TRP C 432 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (25280) covalent geometry : angle 0.62058 / 0.31 (34270) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.50722 / 0.25 ( 8) hydrogen bonds : bond 0.03172 / 2.12 ( 1096) hydrogen bonds : angle 3.72405 / 2.55 ( 3234) Misc. bond : bond 0.00059 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 341 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7683 (tp) cc_final: 0.6724 (mp) REVERT: A 223 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7187 (mmm160) REVERT: A 326 LYS cc_start: 0.8547 (mttp) cc_final: 0.7964 (mtmm) REVERT: A 564 MET cc_start: 0.6555 (mmm) cc_final: 0.5583 (mtp) REVERT: A 569 ASN cc_start: 0.8087 (m110) cc_final: 0.7684 (p0) REVERT: A 582 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8524 (t70) REVERT: A 636 GLN cc_start: 0.8330 (tt0) cc_final: 0.8055 (mt0) REVERT: A 794 ARG cc_start: 0.5238 (mtt90) cc_final: 0.4858 (ttp-170) REVERT: A 812 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6536 (pp20) REVERT: B 62 LEU cc_start: 0.9494 (mm) cc_final: 0.9287 (mp) REVERT: B 123 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.3715 (ttp80) REVERT: B 483 MET cc_start: 0.6792 (mmm) cc_final: 0.6480 (tpp) REVERT: B 569 ASN cc_start: 0.8113 (m110) cc_final: 0.7884 (m-40) REVERT: B 581 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8737 (mt) REVERT: B 664 PHE cc_start: 0.8511 (m-10) cc_final: 0.8206 (m-10) REVERT: B 733 ILE cc_start: 0.8896 (mp) cc_final: 0.8631 (mt) REVERT: C 67 LYS cc_start: 0.8530 (tptt) cc_final: 0.8229 (mmtp) REVERT: C 223 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7019 (mmm160) REVERT: C 326 LYS cc_start: 0.8546 (mttp) cc_final: 0.7957 (mtmm) REVERT: C 564 MET cc_start: 0.6602 (mmm) cc_final: 0.5606 (mtp) REVERT: C 582 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8514 (t70) REVERT: C 794 ARG cc_start: 0.5194 (mtt90) cc_final: 0.4632 (ttp80) REVERT: C 812 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6575 (pp20) REVERT: D 123 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.3829 (ttp80) REVERT: D 483 MET cc_start: 0.6482 (tpp) cc_final: 0.6078 (tpp) REVERT: D 569 ASN cc_start: 0.8188 (m110) cc_final: 0.7901 (m-40) REVERT: D 664 PHE cc_start: 0.8500 (m-10) cc_final: 0.8227 (m-10) REVERT: D 733 ILE cc_start: 0.8887 (mp) cc_final: 0.8620 (mt) outliers start: 83 outliers final: 66 residues processed: 398 average time/residue: 0.1530 time to fit residues: 100.7350 Evaluate side-chains 404 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 331 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 14 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 75 optimal weight: 0.0670 chunk 226 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.156215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.115579 restraints weight = 30174.442| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.81 r_work: 0.2897 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25288 Z= 0.167 Angle : 0.646 14.035 34278 Z= 0.325 Chirality : 0.041 0.168 3888 Planarity : 0.005 0.075 4220 Dihedral : 9.909 167.997 3634 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.32 % Favored : 90.28 % Rotamer: Outliers : 3.60 % Allowed : 16.56 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.34 (0.16), residues: 3004 helix: 0.23 (0.12), residues: 1986 sheet: None (None), residues: 0 loop : -3.19 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 828 TYR 0.021 0.002 TYR C 747 PHE 0.017 0.001 PHE C 723 TRP 0.019 0.001 TRP A 432 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (25280) covalent geometry : angle 0.64620 / 0.32 (34270) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.77171 / 0.37 ( 8) hydrogen bonds : bond 0.03461 / 2.31 ( 1096) hydrogen bonds : angle 3.77843 / 2.58 ( 3234) Misc. bond : bond 0.00078 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 337 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: A 326 LYS cc_start: 0.8574 (mttp) cc_final: 0.8001 (mtmm) REVERT: A 564 MET cc_start: 0.6591 (mmm) cc_final: 0.5687 (mtp) REVERT: A 569 ASN cc_start: 0.8123 (m110) cc_final: 0.7727 (p0) REVERT: A 582 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8613 (t70) REVERT: A 636 GLN cc_start: 0.8370 (tt0) cc_final: 0.8103 (mt0) REVERT: A 812 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6536 (pp20) REVERT: B 62 LEU cc_start: 0.9548 (mm) cc_final: 0.9325 (mp) REVERT: B 101 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8204 (pp) REVERT: B 123 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.3882 (ttp80) REVERT: B 338 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: B 483 MET cc_start: 0.6910 (mmm) cc_final: 0.6659 (tpp) REVERT: B 552 VAL cc_start: 0.8124 (t) cc_final: 0.7869 (p) REVERT: B 569 ASN cc_start: 0.8150 (m110) cc_final: 0.7939 (m-40) REVERT: B 664 PHE cc_start: 0.8633 (m-10) cc_final: 0.8338 (m-10) REVERT: B 733 ILE cc_start: 0.8940 (mp) cc_final: 0.8681 (mt) REVERT: C 67 LYS cc_start: 0.8573 (tptt) cc_final: 0.8288 (mmtp) REVERT: C 223 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7088 (mmm160) REVERT: C 326 LYS cc_start: 0.8560 (mttp) cc_final: 0.7984 (mtmm) REVERT: C 564 MET cc_start: 0.6593 (mmm) cc_final: 0.5701 (mtp) REVERT: C 569 ASN cc_start: 0.8246 (m110) cc_final: 0.7807 (p0) REVERT: C 582 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8594 (t70) REVERT: C 794 ARG cc_start: 0.5252 (mtt90) cc_final: 0.4960 (ttp-170) REVERT: C 812 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6572 (pp20) REVERT: D 101 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8227 (pp) REVERT: D 123 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.3793 (ttp80) REVERT: D 338 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: D 483 MET cc_start: 0.6513 (tpp) cc_final: 0.6223 (tpp) REVERT: D 492 ARG cc_start: 0.7453 (mtm180) cc_final: 0.7063 (mtm180) REVERT: D 552 VAL cc_start: 0.8098 (t) cc_final: 0.7855 (p) REVERT: D 569 ASN cc_start: 0.8217 (m110) cc_final: 0.7975 (m-40) REVERT: D 664 PHE cc_start: 0.8673 (m-10) cc_final: 0.8379 (m-10) REVERT: D 733 ILE cc_start: 0.8951 (mp) cc_final: 0.8682 (mt) REVERT: D 742 MET cc_start: 0.8857 (ttp) cc_final: 0.8636 (ttp) outliers start: 94 outliers final: 75 residues processed: 404 average time/residue: 0.1489 time to fit residues: 99.6695 Evaluate side-chains 410 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 325 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 242 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110322 restraints weight = 30755.377| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.83 r_work: 0.2858 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25288 Z= 0.183 Angle : 0.663 14.113 34278 Z= 0.333 Chirality : 0.041 0.170 3888 Planarity : 0.005 0.075 4220 Dihedral : 9.981 167.902 3634 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.22 % Favored : 90.41 % Rotamer: Outliers : 3.40 % Allowed : 17.14 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.30 (0.16), residues: 3004 helix: 0.27 (0.12), residues: 1978 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 828 TYR 0.021 0.002 TYR C 747 PHE 0.013 0.001 PHE B 234 TRP 0.018 0.001 TRP C 432 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (25280) covalent geometry : angle 0.66312 / 0.33 (34270) SS BOND : bond 0.00017 / 0.01 ( 4) SS BOND : angle 0.81245 / 0.39 ( 8) hydrogen bonds : bond 0.03567 / 2.38 ( 1096) hydrogen bonds : angle 3.80333 / 2.60 ( 3234) Misc. bond : bond 0.00077 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 338 time to evaluate : 0.972 Fit side-chains REVERT: A 71 LEU cc_start: 0.7901 (tp) cc_final: 0.6922 (mp) REVERT: A 223 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6867 (mmm160) REVERT: A 326 LYS cc_start: 0.8550 (mttp) cc_final: 0.7994 (mtmm) REVERT: A 582 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8642 (t70) REVERT: A 636 GLN cc_start: 0.8408 (tt0) cc_final: 0.8158 (mt0) REVERT: A 812 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6529 (pp20) REVERT: B 101 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8299 (pp) REVERT: B 123 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.3958 (ttp80) REVERT: B 338 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8606 (pt0) REVERT: B 552 VAL cc_start: 0.8147 (t) cc_final: 0.7889 (p) REVERT: B 569 ASN cc_start: 0.8161 (m110) cc_final: 0.7959 (m-40) REVERT: B 664 PHE cc_start: 0.8760 (m-10) cc_final: 0.8377 (m-10) REVERT: B 733 ILE cc_start: 0.8971 (mp) cc_final: 0.8717 (mt) REVERT: C 67 LYS cc_start: 0.8599 (tptt) cc_final: 0.8321 (mmtp) REVERT: C 223 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6670 (mmm160) REVERT: C 326 LYS cc_start: 0.8557 (mttp) cc_final: 0.7991 (mtmm) REVERT: C 569 ASN cc_start: 0.8263 (m110) cc_final: 0.7880 (p0) REVERT: C 582 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8641 (t70) REVERT: C 794 ARG cc_start: 0.5246 (mtt90) cc_final: 0.4825 (ttp-170) REVERT: D 101 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8280 (pp) REVERT: D 123 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6360 (tpt170) REVERT: D 338 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: D 483 MET cc_start: 0.6579 (tpp) cc_final: 0.6351 (tpp) REVERT: D 492 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7374 (mtm180) REVERT: D 552 VAL cc_start: 0.8139 (t) cc_final: 0.7879 (p) REVERT: D 664 PHE cc_start: 0.8792 (m-10) cc_final: 0.8401 (m-10) REVERT: D 733 ILE cc_start: 0.8999 (mp) cc_final: 0.8742 (mt) outliers start: 89 outliers final: 74 residues processed: 400 average time/residue: 0.1548 time to fit residues: 101.7840 Evaluate side-chains 412 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 328 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 452 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 776 CYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 67 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 280 optimal weight: 0.0570 chunk 271 optimal weight: 4.9990 chunk 222 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 855 ASN B 603 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 855 ASN D 569 ASN D 603 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116407 restraints weight = 30411.756| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.84 r_work: 0.2999 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25288 Z= 0.107 Angle : 0.600 13.784 34278 Z= 0.303 Chirality : 0.038 0.162 3888 Planarity : 0.004 0.077 4220 Dihedral : 10.749 171.719 3634 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.56 % Favored : 91.18 % Rotamer: Outliers : 2.07 % Allowed : 18.63 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.82 (0.16), residues: 3004 helix: 0.67 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -3.07 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 828 TYR 0.020 0.001 TYR C 747 PHE 0.020 0.001 PHE C 723 TRP 0.009 0.001 TRP C 125 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (25280) covalent geometry : angle 0.59996 / 0.30 (34270) SS BOND : bond 0.00027 / 0.01 ( 4) SS BOND : angle 0.59026 / 0.29 ( 8) hydrogen bonds : bond 0.02706 / 1.80 ( 1096) hydrogen bonds : angle 3.59487 / 2.47 ( 3234) Misc. bond : bond 0.00555 / 0.27 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7502 (tp) cc_final: 0.6796 (mp) REVERT: A 119 MET cc_start: 0.8546 (mtm) cc_final: 0.8343 (ptp) REVERT: A 223 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6953 (mmm160) REVERT: A 483 MET cc_start: 0.8708 (mmm) cc_final: 0.7976 (ttp) REVERT: A 569 ASN cc_start: 0.7976 (m110) cc_final: 0.7628 (p0) REVERT: A 582 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8445 (t70) REVERT: A 636 GLN cc_start: 0.8268 (tt0) cc_final: 0.8004 (mt0) REVERT: B 123 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5694 (tpp-160) REVERT: B 483 MET cc_start: 0.6779 (tpp) cc_final: 0.5726 (mtt) REVERT: B 569 ASN cc_start: 0.7967 (m110) cc_final: 0.7694 (m-40) REVERT: B 665 GLN cc_start: 0.7549 (tt0) cc_final: 0.7104 (tt0) REVERT: B 733 ILE cc_start: 0.8855 (mp) cc_final: 0.8595 (mt) REVERT: C 67 LYS cc_start: 0.8505 (tptt) cc_final: 0.8209 (mmtp) REVERT: C 71 LEU cc_start: 0.7614 (tp) cc_final: 0.6842 (mp) REVERT: C 223 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6659 (mmm160) REVERT: C 411 LEU cc_start: 0.8788 (pp) cc_final: 0.8369 (mp) REVERT: C 483 MET cc_start: 0.8604 (mmm) cc_final: 0.7907 (ttp) REVERT: C 569 ASN cc_start: 0.8045 (m110) cc_final: 0.7703 (p0) REVERT: C 582 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.8451 (t70) REVERT: C 812 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6485 (pp20) REVERT: D 123 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5975 (tpp-160) REVERT: D 483 MET cc_start: 0.6443 (tpp) cc_final: 0.5268 (mtt) REVERT: D 552 VAL cc_start: 0.8010 (t) cc_final: 0.7803 (p) REVERT: D 580 ILE cc_start: 0.9064 (mt) cc_final: 0.8801 (mt) REVERT: D 665 GLN cc_start: 0.7594 (tt0) cc_final: 0.7256 (tt0) REVERT: D 733 ILE cc_start: 0.8871 (mp) cc_final: 0.8615 (mt) outliers start: 54 outliers final: 40 residues processed: 406 average time/residue: 0.1423 time to fit residues: 96.5698 Evaluate side-chains 397 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 820 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 257 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS B 603 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 603 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116017 restraints weight = 30190.788| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.84 r_work: 0.2911 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25288 Z= 0.174 Angle : 0.660 13.933 34278 Z= 0.329 Chirality : 0.041 0.168 3888 Planarity : 0.005 0.076 4220 Dihedral : 10.609 169.260 3634 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.19 % Favored : 90.55 % Rotamer: Outliers : 2.22 % Allowed : 19.01 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.94 (0.16), residues: 3004 helix: 0.57 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 560 TYR 0.024 0.002 TYR D 500 PHE 0.017 0.001 PHE A 523 TRP 0.021 0.001 TRP C 125 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (25280) covalent geometry : angle 0.65993 / 0.33 (34270) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 0.67205 / 0.33 ( 8) hydrogen bonds : bond 0.03397 / 2.27 ( 1096) hydrogen bonds : angle 3.75296 / 2.56 ( 3234) Misc. bond : bond 0.00552 / 0.27 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6660.93 seconds wall clock time: 114 minutes 46.06 seconds (6886.06 seconds total)