Starting phenix.real_space_refine on Thu Mar 5 17:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ows_20216/03_2026/6ows_20216.map" } resolution = 2.98 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= -0.000 sd= 1.000 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 6 5.49 5 S 135 5.16 5 C 15317 2.51 5 N 3825 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "C" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Time building chain proxies: 5.63, per 1000 atoms: 0.24 Number of scatterers: 23651 At special positions: 0 Unit cell: (116.6, 120.84, 142.04, 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 135 16.00 P 6 15.00 O 4368 8.00 N 3825 7.00 C 15317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 24 sheets defined 55.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 4.272A pdb=" N PHE A 5 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 6 " --> pdb=" O GLN A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 6' Processing helix chain 'A' and resid 8 through 25 removed outlier: 3.737A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.544A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.635A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.684A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.928A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.714A pdb=" N VAL A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.725A pdb=" N PHE A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.593A pdb=" N ASP A 264 " --> pdb=" O LYS A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.560A pdb=" N GLU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.511A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 4.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 386 removed outlier: 3.856A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.450A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 4.484A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 removed outlier: 3.647A pdb=" N SER A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.938A pdb=" N LEU A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.540A pdb=" N PHE A 458 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 3.787A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.945A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.979A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.606A pdb=" N VAL A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 635 through 647 removed outlier: 3.573A pdb=" N MET A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 removed outlier: 3.684A pdb=" N LEU A 666 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 667 " --> pdb=" O ASP A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 667' Processing helix chain 'A' and resid 683 through 698 removed outlier: 4.057A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 removed outlier: 3.556A pdb=" N LEU A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.632A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.783A pdb=" N ARG A 771 " --> pdb=" O ALA A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 773 through 779 removed outlier: 3.688A pdb=" N ASP A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 778 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 779 " --> pdb=" O ASP A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 839 removed outlier: 3.893A pdb=" N GLU A 836 " --> pdb=" O MET A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.603A pdb=" N GLN A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.508A pdb=" N MET A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 895 through 909 removed outlier: 3.633A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.587A pdb=" N ALA A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 960 removed outlier: 3.655A pdb=" N THR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 987 through 1009 removed outlier: 4.033A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 3.791A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 4.272A pdb=" N PHE B 5 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 6 " --> pdb=" O GLN B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.736A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.544A pdb=" N ASP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.634A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.683A pdb=" N VAL B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.927A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.713A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.727A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 removed outlier: 3.594A pdb=" N ASP B 264 " --> pdb=" O LYS B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.560A pdb=" N GLU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.511A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.063A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.855A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.450A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 removed outlier: 4.484A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 451 removed outlier: 3.647A pdb=" N SER B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.041A pdb=" N LEU B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.541A pdb=" N PHE B 458 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 487 removed outlier: 3.787A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.945A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 removed outlier: 3.979A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.607A pdb=" N VAL B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 635 through 647 removed outlier: 3.573A pdb=" N MET B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.684A pdb=" N LEU B 666 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 667 " --> pdb=" O ASP B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 667' Processing helix chain 'B' and resid 683 through 698 removed outlier: 4.058A pdb=" N ASP B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.633A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 3.784A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.688A pdb=" N ASP B 776 " --> pdb=" O GLN B 773 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 778 " --> pdb=" O LYS B 775 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 779 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 839 removed outlier: 3.892A pdb=" N GLU B 836 " --> pdb=" O MET B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.602A pdb=" N GLN B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 862 " --> pdb=" O LYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 883 removed outlier: 3.508A pdb=" N MET B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 875 " --> pdb=" O SER B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'B' and resid 895 through 909 removed outlier: 3.634A pdb=" N GLY B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.569A pdb=" N ALA B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 960 removed outlier: 3.656A pdb=" N THR B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 955 " --> pdb=" O ILE B 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 974 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 987 through 1009 removed outlier: 4.032A pdb=" N LEU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1021 removed outlier: 3.792A pdb=" N ILE B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B1020 " --> pdb=" O PHE B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 4.273A pdb=" N PHE C 5 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 6 " --> pdb=" O GLN C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.737A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.544A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.634A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.684A pdb=" N VAL C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.927A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.715A pdb=" N VAL C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.726A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.593A pdb=" N ASP C 264 " --> pdb=" O LYS C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 298 through 313 removed outlier: 3.560A pdb=" N GLU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.511A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 4.064A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.857A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 375 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.449A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 removed outlier: 4.484A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 451 removed outlier: 3.646A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.041A pdb=" N LEU C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.540A pdb=" N PHE C 458 " --> pdb=" O PRO C 455 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.786A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.945A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 3.979A pdb=" N PHE C 513 " --> pdb=" O PHE C 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 525 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.605A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 542 " --> pdb=" O MET C 538 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 544 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 549 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP C 556 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 635 through 647 removed outlier: 3.573A pdb=" N MET C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 removed outlier: 3.684A pdb=" N LEU C 666 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 667 " --> pdb=" O ASP C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 667' Processing helix chain 'C' and resid 683 through 698 removed outlier: 4.056A pdb=" N ASP C 692 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 733 through 738 removed outlier: 3.633A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 removed outlier: 3.784A pdb=" N ARG C 771 " --> pdb=" O ALA C 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 768 through 771' Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.687A pdb=" N ASP C 776 " --> pdb=" O GLN C 773 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 778 " --> pdb=" O LYS C 775 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 779 " --> pdb=" O ASP C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 839 removed outlier: 3.893A pdb=" N GLU C 836 " --> pdb=" O MET C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.603A pdb=" N GLN C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 862 " --> pdb=" O LYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.506A pdb=" N MET C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 875 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 895 through 909 removed outlier: 3.635A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 905 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.588A pdb=" N ALA C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 960 removed outlier: 3.656A pdb=" N THR C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 955 " --> pdb=" O ILE C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 956 " --> pdb=" O GLU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 974 Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 987 through 1009 removed outlier: 4.032A pdb=" N LEU C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1021 removed outlier: 3.792A pdb=" N ILE C1017 " --> pdb=" O PRO C1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 673 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 851 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.532A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.224A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 620 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.922A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 760 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 752 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 762 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 219 removed outlier: 8.001A pdb=" N LEU C 720 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE C 722 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLN A 237 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 715 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 801 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 3.559A pdb=" N ASN A 801 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 715 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE A 722 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B 673 " --> pdb=" O THR B 851 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 851 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.531A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.225A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 620 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.922A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 760 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP B 752 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 762 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 3.558A pdb=" N ASN B 801 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 715 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 722 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 8.040A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER C 673 " --> pdb=" O THR C 851 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 851 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.530A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.224A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 620 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.923A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN C 760 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP C 752 " --> pdb=" O GLN C 760 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 762 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1189 hydrogen bonds defined for protein. 3414 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: 5.29 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3864 1.28 - 1.41: 5389 1.41 - 1.54: 14475 1.54 - 1.68: 83 1.68 - 1.81: 264 Bond restraints: 24075 Sorted by residual: bond pdb=" C LYS C 468 " pdb=" O LYS C 468 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.15e-02 7.56e+03 5.39e+01 bond pdb=" CA ASP B 578 " pdb=" C ASP B 578 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.29e-02 6.01e+03 4.27e+01 bond pdb=" C ALA A 579 " pdb=" O ALA A 579 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.21e-02 6.83e+03 4.21e+01 bond pdb=" C ASP B 578 " pdb=" O ASP B 578 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" C ALA C 579 " pdb=" O ALA C 579 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.22e-02 6.72e+03 3.13e+01 ... (remaining 24070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 32182 3.54 - 7.08: 356 7.08 - 10.62: 50 10.62 - 14.16: 5 14.16 - 17.70: 8 Bond angle restraints: 32601 Sorted by residual: angle pdb=" C LEU B 222 " pdb=" N PRO B 223 " pdb=" CA PRO B 223 " ideal model delta sigma weight residual 119.76 103.76 16.00 1.03e+00 9.43e-01 2.41e+02 angle pdb=" N PRO B 223 " pdb=" CA PRO B 223 " pdb=" C PRO B 223 " ideal model delta sigma weight residual 111.14 96.82 14.32 1.56e+00 4.11e-01 8.42e+01 angle pdb=" N ARG C 724 " pdb=" CA ARG C 724 " pdb=" C ARG C 724 " ideal model delta sigma weight residual 111.28 119.81 -8.53 1.09e+00 8.42e-01 6.12e+01 angle pdb=" N ARG B 724 " pdb=" CA ARG B 724 " pdb=" C ARG B 724 " ideal model delta sigma weight residual 111.28 118.83 -7.55 1.09e+00 8.42e-01 4.79e+01 angle pdb=" N ARG A 724 " pdb=" CA ARG A 724 " pdb=" C ARG A 724 " ideal model delta sigma weight residual 111.28 118.77 -7.49 1.09e+00 8.42e-01 4.72e+01 ... (remaining 32596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 13659 24.86 - 49.72: 848 49.72 - 74.58: 107 74.58 - 99.43: 14 99.43 - 124.29: 3 Dihedral angle restraints: 14631 sinusoidal: 5790 harmonic: 8841 Sorted by residual: dihedral pdb=" CA ASP C 221 " pdb=" C ASP C 221 " pdb=" N LEU C 222 " pdb=" CA LEU C 222 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP A 221 " pdb=" C ASP A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta harmonic sigma weight residual -180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ARG B 632 " pdb=" C ARG B 632 " pdb=" N THR B 633 " pdb=" CA THR B 633 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3732 0.121 - 0.242: 131 0.242 - 0.364: 8 0.364 - 0.485: 6 0.485 - 0.606: 2 Chirality restraints: 3879 Sorted by residual: chirality pdb=" CA TYR B 883 " pdb=" N TYR B 883 " pdb=" C TYR B 883 " pdb=" CB TYR B 883 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.19e+00 chirality pdb=" CA TYR C 883 " pdb=" N TYR C 883 " pdb=" C TYR C 883 " pdb=" CB TYR C 883 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA ARG C 724 " pdb=" N ARG C 724 " pdb=" C ARG C 724 " pdb=" CB ARG C 724 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 3876 not shown) Planarity restraints: 4086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 883 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR B 883 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR B 883 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 884 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 576 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C PRO B 576 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO B 576 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 577 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 575 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C LEU C 575 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 575 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO C 576 " 0.020 2.00e-02 2.50e+03 ... (remaining 4083 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4081 2.75 - 3.29: 20951 3.29 - 3.83: 36579 3.83 - 4.36: 44708 4.36 - 4.90: 77190 Nonbonded interactions: 183509 Sorted by model distance: nonbonded pdb=" NZ LYS C 468 " pdb=" O13 PTY C1102 " model vdw 2.216 3.120 nonbonded pdb=" O THR C 471 " pdb=" OG SER C 475 " model vdw 2.230 3.040 nonbonded pdb=" O THR A 471 " pdb=" OG SER A 475 " model vdw 2.230 3.040 nonbonded pdb=" O THR B 471 " pdb=" OG SER B 475 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 723 " pdb=" OE1 GLU C 725 " model vdw 2.233 3.040 ... (remaining 183504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or resid 1102)) selection = (chain 'C' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) } 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: 8.010 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.990 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 24075 Z= 0.450 Angle : 1.042 17.700 32601 Z= 0.562 Chirality : 0.061 0.606 3879 Planarity : 0.008 0.081 4086 Dihedral : 15.742 124.293 8913 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 6.03 % Allowed : 6.81 % Favored : 87.16 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.11), residues: 3063 helix: -4.36 (0.06), residues: 1530 sheet: -2.77 (0.19), residues: 498 loop : -2.16 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.039 0.002 TYR C 883 PHE 0.022 0.002 PHE A 569 TRP 0.010 0.002 TRP B 800 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00900 (24075) covalent geometry : angle 1.04246 (32601) hydrogen bonds : bond 0.32282 ( 1132) hydrogen bonds : angle 9.67988 ( 3414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 521 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8991 (mt0) cc_final: 0.8682 (mt0) REVERT: A 79 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 89 GLU cc_start: 0.7775 (tt0) cc_final: 0.7457 (tp30) REVERT: A 102 MET cc_start: 0.8364 (mmm) cc_final: 0.8156 (mmt) REVERT: A 128 GLN cc_start: 0.7764 (mp10) cc_final: 0.7402 (mp10) REVERT: A 130 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6393 (pp20) REVERT: A 132 SER cc_start: 0.7857 (t) cc_final: 0.7644 (m) REVERT: A 164 GLU cc_start: 0.8004 (tp30) cc_final: 0.7787 (mm-30) REVERT: A 357 LEU cc_start: 0.8114 (mm) cc_final: 0.7648 (tp) REVERT: A 404 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 517 PHE cc_start: 0.6539 (t80) cc_final: 0.6335 (t80) REVERT: A 525 GLU cc_start: 0.8198 (tt0) cc_final: 0.7818 (tp30) REVERT: A 529 LEU cc_start: 0.8832 (tp) cc_final: 0.8629 (mm) REVERT: A 637 SER cc_start: 0.8323 (t) cc_final: 0.8002 (m) REVERT: A 783 MET cc_start: 0.9017 (tpt) cc_final: 0.8717 (tpp) REVERT: A 844 LYS cc_start: 0.8584 (tttm) cc_final: 0.8108 (mppt) REVERT: A 861 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7548 (mp0) REVERT: A 864 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6864 (tpp) REVERT: A 949 SER cc_start: 0.7196 (OUTLIER) cc_final: 0.6994 (p) REVERT: B 1 MET cc_start: 0.4830 (mmm) cc_final: 0.3912 (mpp) REVERT: B 128 GLN cc_start: 0.7939 (mp10) cc_final: 0.7473 (mp10) REVERT: B 138 MET cc_start: 0.8882 (ptm) cc_final: 0.8647 (ptm) REVERT: B 357 LEU cc_start: 0.8178 (mm) cc_final: 0.7666 (tp) REVERT: B 379 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8149 (t) REVERT: B 404 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8054 (pt) REVERT: B 420 MET cc_start: 0.8746 (mtm) cc_final: 0.7950 (mtp) REVERT: B 637 SER cc_start: 0.8400 (t) cc_final: 0.8104 (m) REVERT: B 656 MET cc_start: 0.8249 (mmm) cc_final: 0.7825 (tpp) REVERT: B 706 MET cc_start: 0.5808 (ttt) cc_final: 0.5502 (mtp) REVERT: B 745 MET cc_start: 0.8220 (mtm) cc_final: 0.7792 (mtm) REVERT: B 770 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 844 LYS cc_start: 0.8800 (tttm) cc_final: 0.8152 (mppt) REVERT: B 861 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 872 MET cc_start: 0.8201 (mtp) cc_final: 0.7986 (mtm) REVERT: B 904 ILE cc_start: 0.7908 (pt) cc_final: 0.7631 (pp) REVERT: B 967 MET cc_start: 0.8833 (mtp) cc_final: 0.8585 (mtp) REVERT: C 67 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8022 (ttm-80) REVERT: C 128 GLN cc_start: 0.7814 (mp10) cc_final: 0.7537 (mp10) REVERT: C 130 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6431 (pp20) REVERT: C 184 MET cc_start: 0.9157 (tpp) cc_final: 0.8938 (tpp) REVERT: C 292 GLN cc_start: 0.8800 (mt0) cc_final: 0.8452 (mt0) REVERT: C 321 MET cc_start: 0.8729 (mtt) cc_final: 0.8496 (mtt) REVERT: C 379 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (t) REVERT: C 404 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (pt) REVERT: C 420 MET cc_start: 0.8687 (mtm) cc_final: 0.8278 (mtm) REVERT: C 454 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 458 PHE cc_start: 0.8684 (m-80) cc_final: 0.8479 (m-80) REVERT: C 529 LEU cc_start: 0.8969 (tp) cc_final: 0.8573 (mm) REVERT: C 637 SER cc_start: 0.8419 (t) cc_final: 0.8098 (m) REVERT: C 639 MET cc_start: 0.8075 (ttm) cc_final: 0.7780 (mtm) REVERT: C 656 MET cc_start: 0.8182 (mmm) cc_final: 0.7456 (tpp) REVERT: C 783 MET cc_start: 0.9096 (tpt) cc_final: 0.8855 (tpp) REVERT: C 813 ARG cc_start: 0.8402 (mmt90) cc_final: 0.8191 (mpt-90) REVERT: C 844 LYS cc_start: 0.8699 (tttm) cc_final: 0.8210 (mmmt) REVERT: C 861 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 864 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6809 (tpp) REVERT: C 915 ASP cc_start: 0.8073 (p0) cc_final: 0.7856 (p0) REVERT: C 942 MET cc_start: 0.7906 (ttm) cc_final: 0.7703 (tmt) outliers start: 155 outliers final: 31 residues processed: 639 average time/residue: 0.6322 time to fit residues: 463.8781 Evaluate side-chains 347 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 237 GLN A 248 ASN A 361 ASN A 586 ASN A 593 ASN A 617 GLN A 644 ASN A 779 ASN A 788 GLN B 44 ASN B 120 GLN B 205 ASN B 237 GLN B 248 ASN B 292 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 586 ASN B 593 ASN B 617 GLN B 644 ASN B 701 ASN B 779 ASN C 44 ASN C 74 ASN C 120 GLN C 205 ASN C 237 GLN C 248 ASN C 361 ASN C 574 GLN C 586 ASN C 593 ASN C 617 GLN C 644 ASN C 717 ASN C 779 ASN C 805 GLN C 863 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092481 restraints weight = 38751.969| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.22 r_work: 0.3079 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24075 Z= 0.155 Angle : 0.659 10.711 32601 Z= 0.339 Chirality : 0.043 0.162 3879 Planarity : 0.006 0.071 4086 Dihedral : 9.372 114.879 3451 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.58 % Allowed : 15.52 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.13), residues: 3063 helix: -2.39 (0.10), residues: 1641 sheet: -1.97 (0.20), residues: 504 loop : -1.52 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.012 0.001 TYR B 883 PHE 0.024 0.002 PHE A 4 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00352 (24075) covalent geometry : angle 0.65893 (32601) hydrogen bonds : bond 0.05829 ( 1132) hydrogen bonds : angle 4.86283 ( 3414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 337 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.9212 (mt0) cc_final: 0.8893 (mt0) REVERT: A 89 GLU cc_start: 0.8335 (tt0) cc_final: 0.7977 (tp30) REVERT: A 128 GLN cc_start: 0.7942 (mp10) cc_final: 0.7521 (mp10) REVERT: A 357 LEU cc_start: 0.8188 (mm) cc_final: 0.7947 (tt) REVERT: A 525 GLU cc_start: 0.8304 (tt0) cc_final: 0.7764 (tp30) REVERT: A 529 LEU cc_start: 0.8640 (tp) cc_final: 0.8315 (mm) REVERT: A 590 GLN cc_start: 0.8320 (tp40) cc_final: 0.7580 (tp-100) REVERT: A 637 SER cc_start: 0.8667 (t) cc_final: 0.8357 (m) REVERT: A 649 ASN cc_start: 0.8559 (m110) cc_final: 0.8042 (p0) REVERT: A 656 MET cc_start: 0.8711 (tpt) cc_final: 0.8463 (tpt) REVERT: A 706 MET cc_start: 0.7086 (mtp) cc_final: 0.6063 (tpp) REVERT: A 783 MET cc_start: 0.9356 (tpt) cc_final: 0.9119 (tpp) REVERT: A 844 LYS cc_start: 0.8788 (tttm) cc_final: 0.8121 (mppt) REVERT: A 849 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 864 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: A 893 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8427 (mmp) REVERT: A 938 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: A 963 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7877 (ttt180) REVERT: B 1 MET cc_start: 0.5130 (mmm) cc_final: 0.4092 (mpp) REVERT: B 112 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8278 (ptpt) REVERT: B 128 GLN cc_start: 0.7798 (mp10) cc_final: 0.7451 (mp10) REVERT: B 138 MET cc_start: 0.8864 (ptm) cc_final: 0.8660 (ptm) REVERT: B 164 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8222 (pm20) REVERT: B 184 MET cc_start: 0.9361 (tpp) cc_final: 0.9052 (tpp) REVERT: B 199 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 235 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8577 (m) REVERT: B 259 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8942 (m) REVERT: B 292 GLN cc_start: 0.8585 (mt0) cc_final: 0.8277 (mt0) REVERT: B 525 GLU cc_start: 0.8375 (tt0) cc_final: 0.7970 (tp30) REVERT: B 529 LEU cc_start: 0.8550 (mt) cc_final: 0.8303 (mm) REVERT: B 538 MET cc_start: 0.7088 (mmm) cc_final: 0.6719 (mtp) REVERT: B 553 MET cc_start: 0.8496 (mtp) cc_final: 0.8033 (mmp) REVERT: B 590 GLN cc_start: 0.8323 (tp40) cc_final: 0.7748 (tp-100) REVERT: B 637 SER cc_start: 0.8691 (t) cc_final: 0.8379 (m) REVERT: B 706 MET cc_start: 0.6603 (ttt) cc_final: 0.6138 (mtp) REVERT: B 745 MET cc_start: 0.8514 (mtm) cc_final: 0.8181 (mtm) REVERT: B 824 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6936 (p90) REVERT: B 844 LYS cc_start: 0.8982 (tttm) cc_final: 0.8336 (mmpt) REVERT: B 904 ILE cc_start: 0.8470 (pt) cc_final: 0.8223 (pp) REVERT: B 963 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8018 (ttt-90) REVERT: C 7 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7527 (ptt90) REVERT: C 112 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8002 (ptpt) REVERT: C 128 GLN cc_start: 0.7808 (mp10) cc_final: 0.7594 (mp10) REVERT: C 292 GLN cc_start: 0.8723 (mt0) cc_final: 0.8412 (mt0) REVERT: C 321 MET cc_start: 0.9000 (mtt) cc_final: 0.8659 (mtt) REVERT: C 355 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8056 (mtp) REVERT: C 420 MET cc_start: 0.8428 (mtm) cc_final: 0.8218 (mtp) REVERT: C 449 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 538 MET cc_start: 0.7075 (mmm) cc_final: 0.6544 (ttp) REVERT: C 564 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7603 (mm-30) REVERT: C 783 MET cc_start: 0.9372 (tpt) cc_final: 0.9143 (tpp) REVERT: C 824 PHE cc_start: 0.7259 (t80) cc_final: 0.7024 (t80) REVERT: C 835 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8662 (mmm) REVERT: C 844 LYS cc_start: 0.8969 (tttm) cc_final: 0.8186 (mmmt) REVERT: C 864 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7256 (tpp) REVERT: C 942 MET cc_start: 0.8274 (ttm) cc_final: 0.7788 (tmt) REVERT: C 952 GLU cc_start: 0.8452 (mp0) cc_final: 0.8166 (mp0) outliers start: 92 outliers final: 27 residues processed: 397 average time/residue: 0.6838 time to fit residues: 309.0456 Evaluate side-chains 316 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 824 PHE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 156 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 108 GLN B 120 GLN B 604 ASN B 788 GLN B 863 GLN C 120 GLN C 604 ASN C 788 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091405 restraints weight = 38629.788| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.21 r_work: 0.3061 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24075 Z= 0.146 Angle : 0.604 10.378 32601 Z= 0.306 Chirality : 0.042 0.159 3879 Planarity : 0.005 0.055 4086 Dihedral : 7.749 85.228 3406 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.05 % Allowed : 16.73 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.93 (0.14), residues: 3063 helix: -1.05 (0.12), residues: 1617 sheet: -1.35 (0.20), residues: 543 loop : -1.21 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 168 TYR 0.010 0.001 TYR B 883 PHE 0.022 0.001 PHE A 4 TRP 0.007 0.001 TRP C 512 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00343 (24075) covalent geometry : angle 0.60423 (32601) hydrogen bonds : bond 0.04688 ( 1132) hydrogen bonds : angle 4.25918 ( 3414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 291 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5545 (mmm) cc_final: 0.4976 (mpp) REVERT: A 42 GLN cc_start: 0.9260 (mt0) cc_final: 0.8955 (mt0) REVERT: A 89 GLU cc_start: 0.8389 (tt0) cc_final: 0.7967 (tp30) REVERT: A 128 GLN cc_start: 0.7881 (mp10) cc_final: 0.7633 (mp10) REVERT: A 164 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8017 (pm20) REVERT: A 292 GLN cc_start: 0.8814 (mt0) cc_final: 0.8329 (mt0) REVERT: A 338 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: A 357 LEU cc_start: 0.8184 (mm) cc_final: 0.7969 (tt) REVERT: A 425 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5557 (tp) REVERT: A 525 GLU cc_start: 0.8251 (tt0) cc_final: 0.7817 (mm-30) REVERT: A 529 LEU cc_start: 0.8559 (tp) cc_final: 0.8152 (mm) REVERT: A 590 GLN cc_start: 0.8220 (tp40) cc_final: 0.7681 (mt0) REVERT: A 649 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.7961 (p0) REVERT: A 783 MET cc_start: 0.9364 (tpt) cc_final: 0.9069 (tpp) REVERT: A 824 PHE cc_start: 0.7114 (t80) cc_final: 0.6790 (p90) REVERT: A 844 LYS cc_start: 0.8812 (tttm) cc_final: 0.8315 (mmpt) REVERT: A 849 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8647 (mt-10) REVERT: A 864 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7111 (tpp) REVERT: A 893 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7876 (mpm) REVERT: A 938 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: B 1 MET cc_start: 0.5351 (mmm) cc_final: 0.4234 (mpp) REVERT: B 68 GLU cc_start: 0.8229 (mp0) cc_final: 0.7938 (mp0) REVERT: B 120 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8600 (mm110) REVERT: B 128 GLN cc_start: 0.7812 (mp10) cc_final: 0.7448 (mp10) REVERT: B 134 SER cc_start: 0.8450 (m) cc_final: 0.8194 (p) REVERT: B 184 MET cc_start: 0.9395 (tpp) cc_final: 0.9091 (tpp) REVERT: B 221 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: B 235 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8594 (m) REVERT: B 292 GLN cc_start: 0.8542 (mt0) cc_final: 0.8224 (mt0) REVERT: B 395 MET cc_start: 0.8399 (mmm) cc_final: 0.8160 (mmp) REVERT: B 425 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5310 (tp) REVERT: B 538 MET cc_start: 0.7239 (mmm) cc_final: 0.6987 (mtp) REVERT: B 553 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8075 (mmp) REVERT: B 590 GLN cc_start: 0.8375 (tp40) cc_final: 0.7807 (mt0) REVERT: B 633 THR cc_start: 0.7475 (p) cc_final: 0.7244 (t) REVERT: B 637 SER cc_start: 0.8724 (t) cc_final: 0.8344 (m) REVERT: B 706 MET cc_start: 0.6716 (ttt) cc_final: 0.6229 (mtp) REVERT: B 824 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.7056 (p90) REVERT: B 844 LYS cc_start: 0.8990 (tttm) cc_final: 0.8383 (mmpt) REVERT: C 1 MET cc_start: 0.5358 (mmm) cc_final: 0.5150 (mmm) REVERT: C 7 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7447 (ptt90) REVERT: C 128 GLN cc_start: 0.7794 (mp10) cc_final: 0.7589 (mp10) REVERT: C 134 SER cc_start: 0.8388 (m) cc_final: 0.8113 (p) REVERT: C 292 GLN cc_start: 0.8731 (mt0) cc_final: 0.8410 (mt0) REVERT: C 425 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5548 (tp) REVERT: C 449 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8596 (tt) REVERT: C 512 TRP cc_start: 0.7493 (t60) cc_final: 0.7206 (t60) REVERT: C 538 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6854 (mtp) REVERT: C 564 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7572 (mm-30) REVERT: C 633 THR cc_start: 0.7605 (p) cc_final: 0.7367 (t) REVERT: C 637 SER cc_start: 0.8520 (t) cc_final: 0.8153 (m) REVERT: C 783 MET cc_start: 0.9360 (tpt) cc_final: 0.9111 (tpp) REVERT: C 824 PHE cc_start: 0.7296 (t80) cc_final: 0.7062 (t80) REVERT: C 835 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8638 (mmm) REVERT: C 844 LYS cc_start: 0.8953 (tttm) cc_final: 0.8190 (mmmt) REVERT: C 861 GLU cc_start: 0.8576 (tp30) cc_final: 0.8086 (tt0) REVERT: C 864 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7261 (tpp) REVERT: C 942 MET cc_start: 0.8277 (ttm) cc_final: 0.7733 (tmt) REVERT: C 943 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7588 (mp) REVERT: C 952 GLU cc_start: 0.8597 (mp0) cc_final: 0.8340 (mp0) REVERT: C 997 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8275 (m) outliers start: 104 outliers final: 30 residues processed: 364 average time/residue: 0.6897 time to fit residues: 284.9614 Evaluate side-chains 316 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 824 PHE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 997 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 129 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 220 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 265 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN B 859 GLN C 120 GLN C 717 ASN C 805 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092326 restraints weight = 38593.246| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.29 r_work: 0.3077 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24075 Z= 0.114 Angle : 0.558 10.645 32601 Z= 0.282 Chirality : 0.041 0.200 3879 Planarity : 0.004 0.049 4086 Dihedral : 7.221 71.129 3403 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.66 % Allowed : 17.66 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3063 helix: -0.37 (0.13), residues: 1623 sheet: -0.90 (0.21), residues: 504 loop : -1.00 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 168 TYR 0.010 0.001 TYR B 883 PHE 0.020 0.001 PHE B 824 TRP 0.005 0.001 TRP B 512 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00263 (24075) covalent geometry : angle 0.55766 (32601) hydrogen bonds : bond 0.03899 ( 1132) hydrogen bonds : angle 4.04542 ( 3414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 293 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5587 (mmm) cc_final: 0.5021 (mpp) REVERT: A 42 GLN cc_start: 0.9292 (mt0) cc_final: 0.8866 (mt0) REVERT: A 89 GLU cc_start: 0.8454 (tt0) cc_final: 0.8045 (tp30) REVERT: A 128 GLN cc_start: 0.7852 (mp10) cc_final: 0.7592 (mp10) REVERT: A 134 SER cc_start: 0.8416 (m) cc_final: 0.8212 (p) REVERT: A 292 GLN cc_start: 0.8805 (mt0) cc_final: 0.8282 (mt0) REVERT: A 338 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: A 425 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5417 (tp) REVERT: A 525 GLU cc_start: 0.8260 (tt0) cc_final: 0.7816 (mm-30) REVERT: A 529 LEU cc_start: 0.8525 (tp) cc_final: 0.8101 (mm) REVERT: A 590 GLN cc_start: 0.8236 (tp40) cc_final: 0.7702 (tt0) REVERT: A 637 SER cc_start: 0.8626 (t) cc_final: 0.8272 (m) REVERT: A 639 MET cc_start: 0.8326 (mtm) cc_final: 0.8006 (mtm) REVERT: A 649 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7874 (p0) REVERT: A 706 MET cc_start: 0.7115 (mtp) cc_final: 0.5687 (tpt) REVERT: A 783 MET cc_start: 0.9371 (tpt) cc_final: 0.9108 (tpp) REVERT: A 824 PHE cc_start: 0.7047 (t80) cc_final: 0.6818 (p90) REVERT: A 844 LYS cc_start: 0.8816 (tttm) cc_final: 0.8177 (mppt) REVERT: A 849 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8656 (mt-10) REVERT: A 864 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7144 (tpp) REVERT: A 888 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7251 (tt) REVERT: A 938 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: B 1 MET cc_start: 0.5465 (mmm) cc_final: 0.4356 (mpp) REVERT: B 68 GLU cc_start: 0.8220 (mp0) cc_final: 0.7789 (mp0) REVERT: B 128 GLN cc_start: 0.7811 (mp10) cc_final: 0.7431 (mp10) REVERT: B 134 SER cc_start: 0.8421 (m) cc_final: 0.8178 (p) REVERT: B 184 MET cc_start: 0.9392 (tpp) cc_final: 0.9066 (tpp) REVERT: B 221 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 235 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8642 (m) REVERT: B 292 GLN cc_start: 0.8495 (mt0) cc_final: 0.8235 (mt0) REVERT: B 395 MET cc_start: 0.8412 (mmm) cc_final: 0.8190 (mmp) REVERT: B 425 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5239 (tp) REVERT: B 483 LEU cc_start: 0.8343 (pp) cc_final: 0.8050 (tt) REVERT: B 529 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7775 (mm) REVERT: B 538 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6961 (mtp) REVERT: B 553 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: B 590 GLN cc_start: 0.8362 (tp40) cc_final: 0.7794 (mt0) REVERT: B 633 THR cc_start: 0.7316 (p) cc_final: 0.7092 (t) REVERT: B 637 SER cc_start: 0.8671 (t) cc_final: 0.8309 (m) REVERT: B 706 MET cc_start: 0.6668 (ttt) cc_final: 0.6194 (mtp) REVERT: B 824 PHE cc_start: 0.7222 (t80) cc_final: 0.6977 (p90) REVERT: B 844 LYS cc_start: 0.8962 (tttm) cc_final: 0.8395 (mmpt) REVERT: C 1 MET cc_start: 0.5540 (mmm) cc_final: 0.5159 (mmm) REVERT: C 7 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7411 (ptt90) REVERT: C 95 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8658 (mtmm) REVERT: C 128 GLN cc_start: 0.7787 (mp10) cc_final: 0.7563 (mp10) REVERT: C 134 SER cc_start: 0.8373 (m) cc_final: 0.8138 (p) REVERT: C 164 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8010 (pm20) REVERT: C 184 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8753 (tpp) REVERT: C 229 LEU cc_start: 0.8239 (mt) cc_final: 0.7687 (mp) REVERT: C 292 GLN cc_start: 0.8718 (mt0) cc_final: 0.8392 (mt0) REVERT: C 425 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5390 (tp) REVERT: C 449 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8604 (tp) REVERT: C 512 TRP cc_start: 0.7547 (t60) cc_final: 0.7301 (t60) REVERT: C 538 MET cc_start: 0.6962 (mmm) cc_final: 0.6715 (mtp) REVERT: C 564 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7534 (mm-30) REVERT: C 633 THR cc_start: 0.7510 (p) cc_final: 0.7280 (t) REVERT: C 637 SER cc_start: 0.8451 (t) cc_final: 0.8092 (m) REVERT: C 783 MET cc_start: 0.9372 (tpt) cc_final: 0.9133 (tpp) REVERT: C 824 PHE cc_start: 0.7292 (t80) cc_final: 0.6970 (p90) REVERT: C 835 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8609 (mmm) REVERT: C 844 LYS cc_start: 0.8939 (tttm) cc_final: 0.8314 (mmpt) REVERT: C 861 GLU cc_start: 0.8602 (tp30) cc_final: 0.8134 (tt0) REVERT: C 864 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7230 (tpp) REVERT: C 907 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7347 (mm) REVERT: C 908 MET cc_start: 0.8708 (mtt) cc_final: 0.8495 (mtt) REVERT: C 942 MET cc_start: 0.8239 (ttm) cc_final: 0.7697 (tmt) REVERT: C 943 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7511 (mp) REVERT: C 997 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8204 (m) outliers start: 94 outliers final: 35 residues processed: 358 average time/residue: 0.6714 time to fit residues: 274.3655 Evaluate side-chains 320 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 86 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089380 restraints weight = 38517.649| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.28 r_work: 0.3027 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24075 Z= 0.170 Angle : 0.609 11.133 32601 Z= 0.305 Chirality : 0.043 0.153 3879 Planarity : 0.004 0.045 4086 Dihedral : 7.067 64.939 3402 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.24 % Allowed : 17.46 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 3063 helix: -0.11 (0.13), residues: 1638 sheet: -0.82 (0.21), residues: 546 loop : -1.01 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.016 0.001 TYR C 883 PHE 0.018 0.001 PHE B 824 TRP 0.006 0.001 TRP A 187 HIS 0.006 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00414 (24075) covalent geometry : angle 0.60911 (32601) hydrogen bonds : bond 0.04396 ( 1132) hydrogen bonds : angle 4.11511 ( 3414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 269 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5814 (mmm) cc_final: 0.5323 (mpp) REVERT: A 67 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: A 89 GLU cc_start: 0.8537 (tt0) cc_final: 0.8162 (tp30) REVERT: A 128 GLN cc_start: 0.7923 (mp10) cc_final: 0.7630 (mp10) REVERT: A 165 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8331 (pp20) REVERT: A 338 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: A 425 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5450 (tp) REVERT: A 525 GLU cc_start: 0.8238 (tt0) cc_final: 0.7982 (mm-30) REVERT: A 529 LEU cc_start: 0.8666 (tp) cc_final: 0.8298 (mm) REVERT: A 590 GLN cc_start: 0.8280 (tp40) cc_final: 0.7750 (tt0) REVERT: A 639 MET cc_start: 0.8432 (mtm) cc_final: 0.8147 (mtm) REVERT: A 649 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7942 (p0) REVERT: A 706 MET cc_start: 0.7457 (mtp) cc_final: 0.6326 (tpp) REVERT: A 783 MET cc_start: 0.9388 (tpt) cc_final: 0.9119 (tpp) REVERT: A 824 PHE cc_start: 0.7194 (t80) cc_final: 0.6986 (p90) REVERT: A 844 LYS cc_start: 0.8754 (tttm) cc_final: 0.8088 (mppt) REVERT: A 849 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8629 (mt-10) REVERT: A 864 MET cc_start: 0.8196 (ttm) cc_final: 0.7070 (tpp) REVERT: A 888 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7291 (tt) REVERT: A 938 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: A 961 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7538 (mtt180) REVERT: B 1 MET cc_start: 0.5801 (mmm) cc_final: 0.4683 (mpp) REVERT: B 4 PHE cc_start: 0.8305 (t80) cc_final: 0.7773 (t80) REVERT: B 67 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.7850 (ptm-80) REVERT: B 68 GLU cc_start: 0.8193 (mp0) cc_final: 0.7543 (mp0) REVERT: B 128 GLN cc_start: 0.7859 (mp10) cc_final: 0.7505 (mp10) REVERT: B 134 SER cc_start: 0.8474 (m) cc_final: 0.8200 (p) REVERT: B 184 MET cc_start: 0.9425 (tpp) cc_final: 0.9139 (tpp) REVERT: B 221 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: B 292 GLN cc_start: 0.8544 (mt0) cc_final: 0.8230 (mt0) REVERT: B 395 MET cc_start: 0.8507 (mmm) cc_final: 0.8294 (mmp) REVERT: B 425 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5779 (tt) REVERT: B 529 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7881 (mm) REVERT: B 538 MET cc_start: 0.7507 (mmm) cc_final: 0.7291 (mtp) REVERT: B 553 MET cc_start: 0.8547 (mtp) cc_final: 0.8081 (mmm) REVERT: B 633 THR cc_start: 0.7426 (p) cc_final: 0.7208 (t) REVERT: B 637 SER cc_start: 0.8467 (t) cc_final: 0.8060 (m) REVERT: B 706 MET cc_start: 0.7095 (ttt) cc_final: 0.6548 (mtp) REVERT: B 824 PHE cc_start: 0.7372 (t80) cc_final: 0.7147 (p90) REVERT: B 844 LYS cc_start: 0.8894 (tttm) cc_final: 0.8368 (mmpt) REVERT: B 888 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7153 (tt) REVERT: B 907 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7398 (mm) REVERT: C 1 MET cc_start: 0.5683 (mmm) cc_final: 0.5326 (mmm) REVERT: C 73 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8778 (ptpp) REVERT: C 128 GLN cc_start: 0.7830 (mp10) cc_final: 0.7608 (mp10) REVERT: C 164 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8048 (pm20) REVERT: C 292 GLN cc_start: 0.8668 (mt0) cc_final: 0.8386 (mt0) REVERT: C 425 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5672 (tp) REVERT: C 449 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8687 (tp) REVERT: C 512 TRP cc_start: 0.7622 (t60) cc_final: 0.7400 (t60) REVERT: C 538 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6722 (mtp) REVERT: C 564 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7523 (mm-30) REVERT: C 633 THR cc_start: 0.7531 (p) cc_final: 0.7292 (t) REVERT: C 637 SER cc_start: 0.8479 (t) cc_final: 0.8059 (m) REVERT: C 706 MET cc_start: 0.7848 (mtp) cc_final: 0.6375 (tpt) REVERT: C 783 MET cc_start: 0.9371 (tpt) cc_final: 0.9148 (tpp) REVERT: C 824 PHE cc_start: 0.7418 (t80) cc_final: 0.7193 (p90) REVERT: C 835 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8598 (mmm) REVERT: C 844 LYS cc_start: 0.8978 (tttm) cc_final: 0.8224 (mmmt) REVERT: C 861 GLU cc_start: 0.8668 (tp30) cc_final: 0.8130 (tt0) REVERT: C 864 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7243 (tpp) REVERT: C 907 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7281 (mm) REVERT: C 942 MET cc_start: 0.8266 (ttm) cc_final: 0.7735 (tmt) REVERT: C 943 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7590 (mp) REVERT: C 997 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8318 (m) outliers start: 109 outliers final: 43 residues processed: 349 average time/residue: 0.7042 time to fit residues: 279.0815 Evaluate side-chains 309 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 262 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 254 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN B 691 GLN C 120 GLN C 691 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091337 restraints weight = 38617.412| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.29 r_work: 0.3062 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24075 Z= 0.115 Angle : 0.562 11.690 32601 Z= 0.279 Chirality : 0.041 0.143 3879 Planarity : 0.004 0.043 4086 Dihedral : 6.586 60.158 3397 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.07 % Allowed : 19.02 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3063 helix: 0.22 (0.13), residues: 1641 sheet: -0.44 (0.22), residues: 510 loop : -0.93 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.011 0.001 TYR B 883 PHE 0.019 0.001 PHE B 824 TRP 0.004 0.001 TRP C 886 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00269 (24075) covalent geometry : angle 0.56173 (32601) hydrogen bonds : bond 0.03702 ( 1132) hydrogen bonds : angle 3.94153 ( 3414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5863 (mmm) cc_final: 0.5392 (mpp) REVERT: A 67 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8048 (ttm-80) REVERT: A 89 GLU cc_start: 0.8450 (tt0) cc_final: 0.8086 (tp30) REVERT: A 120 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8483 (mm110) REVERT: A 128 GLN cc_start: 0.7892 (mp10) cc_final: 0.7628 (mp10) REVERT: A 165 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: A 292 GLN cc_start: 0.8778 (mt0) cc_final: 0.8242 (mt0) REVERT: A 338 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: A 425 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5326 (tp) REVERT: A 525 GLU cc_start: 0.8203 (tt0) cc_final: 0.7992 (mm-30) REVERT: A 529 LEU cc_start: 0.8604 (tp) cc_final: 0.8153 (mm) REVERT: A 590 GLN cc_start: 0.8251 (tp40) cc_final: 0.7727 (tt0) REVERT: A 637 SER cc_start: 0.8490 (t) cc_final: 0.8070 (m) REVERT: A 639 MET cc_start: 0.8390 (mtm) cc_final: 0.8123 (mtm) REVERT: A 649 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7847 (p0) REVERT: A 706 MET cc_start: 0.6987 (mtp) cc_final: 0.5521 (tpt) REVERT: A 783 MET cc_start: 0.9418 (tpt) cc_final: 0.9120 (tpp) REVERT: A 844 LYS cc_start: 0.8781 (tttm) cc_final: 0.8110 (mppt) REVERT: A 849 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8636 (mt-10) REVERT: A 864 MET cc_start: 0.8133 (ttm) cc_final: 0.6985 (tpp) REVERT: A 888 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7281 (tt) REVERT: A 938 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: A 961 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7624 (mtt180) REVERT: B 1 MET cc_start: 0.5844 (mmm) cc_final: 0.5490 (mmm) REVERT: B 4 PHE cc_start: 0.8306 (t80) cc_final: 0.7690 (t80) REVERT: B 67 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7994 (ptm-80) REVERT: B 68 GLU cc_start: 0.8202 (mp0) cc_final: 0.7584 (mp0) REVERT: B 128 GLN cc_start: 0.7840 (mp10) cc_final: 0.7492 (mp10) REVERT: B 134 SER cc_start: 0.8445 (m) cc_final: 0.8172 (p) REVERT: B 184 MET cc_start: 0.9419 (tpp) cc_final: 0.9178 (tpp) REVERT: B 221 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: B 292 GLN cc_start: 0.8498 (mt0) cc_final: 0.8201 (mt0) REVERT: B 395 MET cc_start: 0.8501 (mmm) cc_final: 0.8277 (mmp) REVERT: B 425 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5824 (tt) REVERT: B 529 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7894 (mm) REVERT: B 538 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7255 (mtp) REVERT: B 553 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8013 (mmm) REVERT: B 633 THR cc_start: 0.7385 (p) cc_final: 0.7150 (t) REVERT: B 637 SER cc_start: 0.8379 (t) cc_final: 0.7999 (m) REVERT: B 706 MET cc_start: 0.6725 (ttt) cc_final: 0.6268 (mtp) REVERT: B 844 LYS cc_start: 0.8884 (tttm) cc_final: 0.8346 (mmpt) REVERT: B 888 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7139 (tt) REVERT: B 907 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7381 (mm) REVERT: C 1 MET cc_start: 0.5864 (mmm) cc_final: 0.5482 (mmm) REVERT: C 128 GLN cc_start: 0.7795 (mp10) cc_final: 0.7568 (mp10) REVERT: C 164 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7990 (pm20) REVERT: C 292 GLN cc_start: 0.8674 (mt0) cc_final: 0.8399 (mt0) REVERT: C 425 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5567 (tp) REVERT: C 449 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (tp) REVERT: C 512 TRP cc_start: 0.7630 (t60) cc_final: 0.7401 (t60) REVERT: C 538 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6814 (mtp) REVERT: C 539 MET cc_start: 0.7795 (tpt) cc_final: 0.7493 (mmt) REVERT: C 633 THR cc_start: 0.7532 (p) cc_final: 0.7283 (t) REVERT: C 637 SER cc_start: 0.8427 (t) cc_final: 0.8038 (m) REVERT: C 706 MET cc_start: 0.7363 (mtp) cc_final: 0.5852 (tpt) REVERT: C 783 MET cc_start: 0.9380 (tpt) cc_final: 0.9150 (tpp) REVERT: C 824 PHE cc_start: 0.7291 (t80) cc_final: 0.7051 (p90) REVERT: C 835 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: C 844 LYS cc_start: 0.8959 (tttm) cc_final: 0.8215 (mmmt) REVERT: C 861 GLU cc_start: 0.8719 (tp30) cc_final: 0.8106 (tt0) REVERT: C 864 MET cc_start: 0.8221 (ttm) cc_final: 0.7079 (tpp) REVERT: C 913 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7001 (mpp) REVERT: C 942 MET cc_start: 0.8243 (ttm) cc_final: 0.7740 (tmt) REVERT: C 943 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7521 (mp) REVERT: C 997 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8300 (m) outliers start: 79 outliers final: 33 residues processed: 319 average time/residue: 0.6686 time to fit residues: 243.5780 Evaluate side-chains 299 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 186 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 271 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 230 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092207 restraints weight = 38403.529| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.29 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24075 Z= 0.107 Angle : 0.554 12.015 32601 Z= 0.274 Chirality : 0.040 0.141 3879 Planarity : 0.004 0.042 4086 Dihedral : 6.257 57.452 3394 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.15 % Allowed : 19.06 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.13 (0.16), residues: 3063 helix: 0.45 (0.13), residues: 1647 sheet: -0.40 (0.22), residues: 540 loop : -0.62 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.011 0.001 TYR B 883 PHE 0.014 0.001 PHE B 824 TRP 0.005 0.001 TRP C 886 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00252 (24075) covalent geometry : angle 0.55408 (32601) hydrogen bonds : bond 0.03451 ( 1132) hydrogen bonds : angle 3.84524 ( 3414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 262 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5932 (mmm) cc_final: 0.5387 (mpp) REVERT: A 67 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: A 89 GLU cc_start: 0.8459 (tt0) cc_final: 0.8095 (tp30) REVERT: A 101 GLU cc_start: 0.8564 (tp30) cc_final: 0.8043 (tp30) REVERT: A 128 GLN cc_start: 0.7870 (mp10) cc_final: 0.7607 (mp10) REVERT: A 165 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: A 256 ASN cc_start: 0.8248 (p0) cc_final: 0.8044 (p0) REVERT: A 292 GLN cc_start: 0.8746 (mt0) cc_final: 0.8212 (mt0) REVERT: A 525 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: A 529 LEU cc_start: 0.8626 (tp) cc_final: 0.8221 (mm) REVERT: A 590 GLN cc_start: 0.8207 (tp40) cc_final: 0.7679 (tt0) REVERT: A 637 SER cc_start: 0.8440 (t) cc_final: 0.8043 (m) REVERT: A 649 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7783 (p0) REVERT: A 706 MET cc_start: 0.6963 (mtp) cc_final: 0.5602 (tpt) REVERT: A 783 MET cc_start: 0.9417 (tpt) cc_final: 0.9130 (tpp) REVERT: A 844 LYS cc_start: 0.8770 (tttm) cc_final: 0.8086 (mppt) REVERT: A 849 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8624 (mt-10) REVERT: A 864 MET cc_start: 0.8095 (ttm) cc_final: 0.6945 (tpp) REVERT: A 888 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7209 (tt) REVERT: A 938 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: B 1 MET cc_start: 0.5896 (mmm) cc_final: 0.5544 (mmm) REVERT: B 4 PHE cc_start: 0.8334 (t80) cc_final: 0.7606 (t80) REVERT: B 67 ARG cc_start: 0.8590 (ptm-80) cc_final: 0.8045 (ptm-80) REVERT: B 68 GLU cc_start: 0.8223 (mp0) cc_final: 0.7611 (mp0) REVERT: B 128 GLN cc_start: 0.7854 (mp10) cc_final: 0.7519 (mp10) REVERT: B 134 SER cc_start: 0.8471 (m) cc_final: 0.8191 (p) REVERT: B 184 MET cc_start: 0.9430 (tpp) cc_final: 0.9186 (tpp) REVERT: B 292 GLN cc_start: 0.8474 (mt0) cc_final: 0.8190 (mt0) REVERT: B 353 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 425 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5824 (tt) REVERT: B 529 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7888 (mm) REVERT: B 538 MET cc_start: 0.7361 (mmm) cc_final: 0.7149 (mtp) REVERT: B 553 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: B 633 THR cc_start: 0.7394 (p) cc_final: 0.7172 (t) REVERT: B 637 SER cc_start: 0.8692 (t) cc_final: 0.8317 (m) REVERT: B 706 MET cc_start: 0.6640 (ttt) cc_final: 0.6232 (mtp) REVERT: B 844 LYS cc_start: 0.8848 (tttm) cc_final: 0.8340 (mmpt) REVERT: B 888 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7143 (tt) REVERT: B 907 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7361 (mm) REVERT: C 1 MET cc_start: 0.5989 (mmm) cc_final: 0.5618 (mmm) REVERT: C 102 MET cc_start: 0.7508 (mmt) cc_final: 0.7288 (mmm) REVERT: C 128 GLN cc_start: 0.7775 (mp10) cc_final: 0.7547 (mp10) REVERT: C 164 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8079 (pt0) REVERT: C 165 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8179 (pp20) REVERT: C 292 GLN cc_start: 0.8664 (mt0) cc_final: 0.8374 (mt0) REVERT: C 425 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5526 (tp) REVERT: C 449 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 512 TRP cc_start: 0.7650 (t60) cc_final: 0.7407 (t60) REVERT: C 538 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6734 (mtp) REVERT: C 539 MET cc_start: 0.7807 (tpt) cc_final: 0.7564 (mmt) REVERT: C 633 THR cc_start: 0.7423 (p) cc_final: 0.7124 (t) REVERT: C 637 SER cc_start: 0.8395 (t) cc_final: 0.8000 (m) REVERT: C 706 MET cc_start: 0.7270 (mtp) cc_final: 0.5855 (tpt) REVERT: C 783 MET cc_start: 0.9384 (tpt) cc_final: 0.9158 (tpp) REVERT: C 824 PHE cc_start: 0.7183 (t80) cc_final: 0.6971 (p90) REVERT: C 835 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: C 844 LYS cc_start: 0.8939 (tttm) cc_final: 0.8342 (mmpt) REVERT: C 861 GLU cc_start: 0.8753 (tp30) cc_final: 0.8204 (tt0) REVERT: C 864 MET cc_start: 0.8168 (ttm) cc_final: 0.7042 (tpp) REVERT: C 913 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7055 (mpp) REVERT: C 942 MET cc_start: 0.8256 (ttm) cc_final: 0.7768 (tmt) REVERT: C 943 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 997 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (m) outliers start: 81 outliers final: 37 residues processed: 325 average time/residue: 0.6277 time to fit residues: 233.1321 Evaluate side-chains 300 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 166 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 225 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 42 GLN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089933 restraints weight = 38447.851| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.20 r_work: 0.3036 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24075 Z= 0.172 Angle : 0.605 12.568 32601 Z= 0.300 Chirality : 0.043 0.145 3879 Planarity : 0.004 0.059 4086 Dihedral : 6.300 56.227 3390 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.31 % Allowed : 19.41 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3063 helix: 0.41 (0.13), residues: 1644 sheet: -0.36 (0.22), residues: 546 loop : -0.74 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 67 TYR 0.016 0.001 TYR B 883 PHE 0.015 0.001 PHE A 672 TRP 0.006 0.001 TRP A 187 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00427 (24075) covalent geometry : angle 0.60481 (32601) hydrogen bonds : bond 0.04040 ( 1132) hydrogen bonds : angle 4.00699 ( 3414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 252 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6334 (mmm) cc_final: 0.5734 (mpp) REVERT: A 67 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8009 (ttm-80) REVERT: A 89 GLU cc_start: 0.8479 (tt0) cc_final: 0.8107 (tp30) REVERT: A 101 GLU cc_start: 0.8550 (tp30) cc_final: 0.8038 (tp30) REVERT: A 120 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8614 (mm110) REVERT: A 128 GLN cc_start: 0.7905 (mp10) cc_final: 0.7637 (mp10) REVERT: A 165 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8353 (pp20) REVERT: A 256 ASN cc_start: 0.8228 (p0) cc_final: 0.8017 (p0) REVERT: A 338 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: A 525 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: A 529 LEU cc_start: 0.8601 (tp) cc_final: 0.8228 (mm) REVERT: A 590 GLN cc_start: 0.8221 (tp40) cc_final: 0.7708 (tt0) REVERT: A 649 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7867 (p0) REVERT: A 706 MET cc_start: 0.7316 (mtp) cc_final: 0.6286 (tpp) REVERT: A 783 MET cc_start: 0.9412 (tpt) cc_final: 0.9146 (tpp) REVERT: A 844 LYS cc_start: 0.8734 (tttm) cc_final: 0.8076 (mppt) REVERT: A 849 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8619 (mt-10) REVERT: A 864 MET cc_start: 0.8123 (ttm) cc_final: 0.6928 (tpp) REVERT: A 888 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7277 (tt) REVERT: A 938 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: A 961 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7493 (mtt180) REVERT: B 1 MET cc_start: 0.6099 (mmm) cc_final: 0.5599 (mmm) REVERT: B 4 PHE cc_start: 0.8256 (t80) cc_final: 0.7198 (t80) REVERT: B 67 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8026 (ptm-80) REVERT: B 68 GLU cc_start: 0.8205 (mp0) cc_final: 0.7569 (mp0) REVERT: B 128 GLN cc_start: 0.7876 (mp10) cc_final: 0.7540 (mp10) REVERT: B 184 MET cc_start: 0.9455 (tpp) cc_final: 0.9155 (tpp) REVERT: B 353 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8065 (mp) REVERT: B 538 MET cc_start: 0.7411 (mmm) cc_final: 0.7198 (mtp) REVERT: B 553 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: B 633 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7184 (t) REVERT: B 637 SER cc_start: 0.8525 (t) cc_final: 0.8125 (m) REVERT: B 706 MET cc_start: 0.6972 (ttt) cc_final: 0.6470 (mtp) REVERT: B 756 GLN cc_start: 0.8907 (pt0) cc_final: 0.8653 (pt0) REVERT: B 844 LYS cc_start: 0.8872 (tttm) cc_final: 0.8368 (mmpt) REVERT: B 888 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7028 (tt) REVERT: B 907 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7361 (mm) REVERT: C 1 MET cc_start: 0.6187 (mmm) cc_final: 0.5828 (mmm) REVERT: C 95 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8660 (mtpt) REVERT: C 102 MET cc_start: 0.7596 (mmt) cc_final: 0.7194 (mmm) REVERT: C 128 GLN cc_start: 0.7821 (mp10) cc_final: 0.7587 (mp10) REVERT: C 164 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8077 (pt0) REVERT: C 165 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8396 (pp20) REVERT: C 256 ASN cc_start: 0.8062 (p0) cc_final: 0.7788 (p0) REVERT: C 292 GLN cc_start: 0.8662 (mt0) cc_final: 0.8390 (mt0) REVERT: C 353 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 425 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5672 (tp) REVERT: C 449 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8751 (tp) REVERT: C 512 TRP cc_start: 0.7661 (t60) cc_final: 0.7388 (t60) REVERT: C 529 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7992 (mm) REVERT: C 538 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6878 (mtp) REVERT: C 633 THR cc_start: 0.7369 (p) cc_final: 0.7138 (t) REVERT: C 637 SER cc_start: 0.8477 (t) cc_final: 0.8040 (m) REVERT: C 706 MET cc_start: 0.7564 (mtp) cc_final: 0.6292 (tpt) REVERT: C 783 MET cc_start: 0.9397 (tpt) cc_final: 0.9173 (tpp) REVERT: C 824 PHE cc_start: 0.7350 (t80) cc_final: 0.7140 (p90) REVERT: C 835 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8533 (mmm) REVERT: C 844 LYS cc_start: 0.8946 (tttm) cc_final: 0.8330 (mmpt) REVERT: C 858 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7812 (mmtt) REVERT: C 861 GLU cc_start: 0.8643 (tp30) cc_final: 0.8050 (tt0) REVERT: C 864 MET cc_start: 0.8153 (ttm) cc_final: 0.6985 (tpp) REVERT: C 942 MET cc_start: 0.8182 (ttm) cc_final: 0.7698 (tmt) REVERT: C 997 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (m) outliers start: 85 outliers final: 37 residues processed: 313 average time/residue: 0.6659 time to fit residues: 237.1525 Evaluate side-chains 308 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 858 LYS Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 159 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 303 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 192 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091245 restraints weight = 38462.012| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.21 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24075 Z= 0.125 Angle : 0.581 12.944 32601 Z= 0.287 Chirality : 0.041 0.154 3879 Planarity : 0.004 0.042 4086 Dihedral : 6.163 58.577 3390 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.03 % Allowed : 19.64 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3063 helix: 0.55 (0.13), residues: 1647 sheet: -0.24 (0.22), residues: 546 loop : -0.67 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 67 TYR 0.015 0.001 TYR B 883 PHE 0.014 0.001 PHE A 4 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00302 (24075) covalent geometry : angle 0.58056 (32601) hydrogen bonds : bond 0.03680 ( 1132) hydrogen bonds : angle 3.92384 ( 3414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 250 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6280 (mmm) cc_final: 0.5775 (mpp) REVERT: A 67 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8026 (ttm-80) REVERT: A 89 GLU cc_start: 0.8465 (tt0) cc_final: 0.8105 (tp30) REVERT: A 101 GLU cc_start: 0.8544 (tp30) cc_final: 0.8272 (tp30) REVERT: A 120 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8497 (mm110) REVERT: A 128 GLN cc_start: 0.7859 (mp10) cc_final: 0.7591 (mp10) REVERT: A 165 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: A 256 ASN cc_start: 0.8228 (p0) cc_final: 0.8008 (p0) REVERT: A 338 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 525 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: A 529 LEU cc_start: 0.8587 (tp) cc_final: 0.8205 (mm) REVERT: A 590 GLN cc_start: 0.8236 (tp40) cc_final: 0.7716 (tt0) REVERT: A 649 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7799 (p0) REVERT: A 706 MET cc_start: 0.7073 (mtp) cc_final: 0.5775 (tpt) REVERT: A 783 MET cc_start: 0.9436 (tpt) cc_final: 0.9167 (tpp) REVERT: A 844 LYS cc_start: 0.8772 (tttm) cc_final: 0.8107 (mppt) REVERT: A 849 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8612 (mt-10) REVERT: A 864 MET cc_start: 0.8120 (ttm) cc_final: 0.6926 (tpp) REVERT: A 888 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7267 (tt) REVERT: A 938 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: A 961 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7643 (mtt180) REVERT: B 1 MET cc_start: 0.6193 (mmm) cc_final: 0.5378 (mmm) REVERT: B 4 PHE cc_start: 0.8305 (t80) cc_final: 0.7332 (t80) REVERT: B 68 GLU cc_start: 0.8229 (mp0) cc_final: 0.7627 (mp0) REVERT: B 128 GLN cc_start: 0.7877 (mp10) cc_final: 0.7554 (mp10) REVERT: B 184 MET cc_start: 0.9448 (tpp) cc_final: 0.9156 (tpp) REVERT: B 353 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 529 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 553 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: B 633 THR cc_start: 0.7401 (p) cc_final: 0.7162 (t) REVERT: B 637 SER cc_start: 0.8514 (t) cc_final: 0.8125 (m) REVERT: B 695 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: B 706 MET cc_start: 0.6831 (ttt) cc_final: 0.6335 (mtp) REVERT: B 756 GLN cc_start: 0.8872 (pt0) cc_final: 0.8645 (pt0) REVERT: B 844 LYS cc_start: 0.8849 (tttm) cc_final: 0.8362 (mmpt) REVERT: B 888 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7050 (tt) REVERT: B 893 MET cc_start: 0.8565 (mmp) cc_final: 0.8343 (mmp) REVERT: B 907 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7368 (mm) REVERT: C 1 MET cc_start: 0.6290 (mmm) cc_final: 0.5955 (mmm) REVERT: C 95 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8667 (mtpt) REVERT: C 128 GLN cc_start: 0.7787 (mp10) cc_final: 0.7564 (mp10) REVERT: C 164 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8051 (pt0) REVERT: C 165 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (pp20) REVERT: C 256 ASN cc_start: 0.8035 (p0) cc_final: 0.7790 (p0) REVERT: C 292 GLN cc_start: 0.8651 (mt0) cc_final: 0.8371 (mt0) REVERT: C 353 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 425 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5660 (tp) REVERT: C 449 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8819 (tp) REVERT: C 512 TRP cc_start: 0.7658 (t60) cc_final: 0.7373 (t60) REVERT: C 538 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6769 (mtp) REVERT: C 539 MET cc_start: 0.7761 (tpt) cc_final: 0.7479 (mmt) REVERT: C 633 THR cc_start: 0.7339 (p) cc_final: 0.7112 (t) REVERT: C 706 MET cc_start: 0.7385 (mtp) cc_final: 0.6082 (tpt) REVERT: C 783 MET cc_start: 0.9402 (tpt) cc_final: 0.9187 (tpp) REVERT: C 835 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8562 (mmm) REVERT: C 844 LYS cc_start: 0.8952 (tttm) cc_final: 0.8356 (mmpt) REVERT: C 858 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7827 (mmtt) REVERT: C 861 GLU cc_start: 0.8694 (tp30) cc_final: 0.8133 (tt0) REVERT: C 864 MET cc_start: 0.8139 (ttm) cc_final: 0.6973 (tpp) REVERT: C 942 MET cc_start: 0.8263 (ttm) cc_final: 0.7782 (tmt) REVERT: C 997 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8337 (m) outliers start: 78 outliers final: 38 residues processed: 305 average time/residue: 0.7295 time to fit residues: 252.0658 Evaluate side-chains 303 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 858 LYS Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.0170 chunk 270 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 285 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091383 restraints weight = 38486.670| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.15 r_work: 0.3069 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24075 Z= 0.129 Angle : 0.591 12.954 32601 Z= 0.290 Chirality : 0.042 0.171 3879 Planarity : 0.004 0.045 4086 Dihedral : 6.115 59.319 3390 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.92 % Allowed : 20.07 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3063 helix: 0.58 (0.13), residues: 1650 sheet: -0.19 (0.22), residues: 546 loop : -0.67 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 67 TYR 0.017 0.001 TYR B 883 PHE 0.013 0.001 PHE A 824 TRP 0.006 0.001 TRP C 886 HIS 0.005 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00314 (24075) covalent geometry : angle 0.59114 (32601) hydrogen bonds : bond 0.03686 ( 1132) hydrogen bonds : angle 3.92864 ( 3414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 250 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6304 (mmm) cc_final: 0.5675 (mpp) REVERT: A 67 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: A 89 GLU cc_start: 0.8455 (tt0) cc_final: 0.8088 (tp30) REVERT: A 128 GLN cc_start: 0.7832 (mp10) cc_final: 0.7568 (mp10) REVERT: A 165 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8338 (pp20) REVERT: A 338 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: A 525 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: A 529 LEU cc_start: 0.8595 (tp) cc_final: 0.8207 (mm) REVERT: A 590 GLN cc_start: 0.8225 (tp40) cc_final: 0.7702 (tt0) REVERT: A 649 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7780 (p0) REVERT: A 706 MET cc_start: 0.7024 (mtp) cc_final: 0.5877 (tpt) REVERT: A 783 MET cc_start: 0.9431 (tpt) cc_final: 0.9156 (tpp) REVERT: A 844 LYS cc_start: 0.8759 (tttm) cc_final: 0.8103 (mppt) REVERT: A 849 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8614 (mt-10) REVERT: A 864 MET cc_start: 0.8127 (ttm) cc_final: 0.6920 (tpp) REVERT: A 888 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7290 (tt) REVERT: A 938 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: A 961 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7733 (mtt180) REVERT: B 1 MET cc_start: 0.6187 (mmm) cc_final: 0.5354 (mmm) REVERT: B 4 PHE cc_start: 0.8297 (t80) cc_final: 0.7263 (t80) REVERT: B 67 ARG cc_start: 0.8611 (ptm-80) cc_final: 0.8044 (ptm-80) REVERT: B 68 GLU cc_start: 0.8209 (mp0) cc_final: 0.7621 (mp0) REVERT: B 128 GLN cc_start: 0.7878 (mp10) cc_final: 0.7549 (mp10) REVERT: B 134 SER cc_start: 0.8544 (m) cc_final: 0.8341 (p) REVERT: B 184 MET cc_start: 0.9442 (tpp) cc_final: 0.9143 (tpp) REVERT: B 353 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 529 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8107 (mm) REVERT: B 553 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8001 (mmm) REVERT: B 633 THR cc_start: 0.7403 (p) cc_final: 0.7161 (t) REVERT: B 637 SER cc_start: 0.8502 (t) cc_final: 0.8104 (m) REVERT: B 695 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8172 (mmt) REVERT: B 706 MET cc_start: 0.6859 (ttt) cc_final: 0.6360 (mtp) REVERT: B 844 LYS cc_start: 0.8834 (tttm) cc_final: 0.8358 (mmpt) REVERT: B 888 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7028 (tt) REVERT: B 893 MET cc_start: 0.8568 (mmp) cc_final: 0.8338 (mmp) REVERT: B 907 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7352 (mm) REVERT: C 1 MET cc_start: 0.6379 (mmm) cc_final: 0.6048 (mmm) REVERT: C 95 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8667 (mtpt) REVERT: C 128 GLN cc_start: 0.7778 (mp10) cc_final: 0.7557 (mp10) REVERT: C 164 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8025 (pt0) REVERT: C 165 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8555 (pp20) REVERT: C 256 ASN cc_start: 0.8035 (p0) cc_final: 0.7770 (p0) REVERT: C 292 GLN cc_start: 0.8641 (mt0) cc_final: 0.8362 (mt0) REVERT: C 353 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 425 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5632 (tp) REVERT: C 449 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8808 (tp) REVERT: C 512 TRP cc_start: 0.7593 (t60) cc_final: 0.7287 (t60) REVERT: C 529 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7943 (mm) REVERT: C 538 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6745 (mtp) REVERT: C 539 MET cc_start: 0.7752 (tpt) cc_final: 0.7475 (mmt) REVERT: C 633 THR cc_start: 0.7355 (p) cc_final: 0.7115 (t) REVERT: C 637 SER cc_start: 0.8466 (t) cc_final: 0.8047 (m) REVERT: C 706 MET cc_start: 0.7467 (mtp) cc_final: 0.6138 (tpt) REVERT: C 783 MET cc_start: 0.9401 (tpt) cc_final: 0.9185 (tpp) REVERT: C 835 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8552 (mmm) REVERT: C 844 LYS cc_start: 0.8934 (tttm) cc_final: 0.8358 (mmpt) REVERT: C 858 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7880 (tptm) REVERT: C 861 GLU cc_start: 0.8682 (tp30) cc_final: 0.8115 (tt0) REVERT: C 864 MET cc_start: 0.8145 (ttm) cc_final: 0.6954 (tpp) REVERT: C 942 MET cc_start: 0.8261 (ttm) cc_final: 0.7767 (tmt) REVERT: C 997 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (m) outliers start: 75 outliers final: 44 residues processed: 303 average time/residue: 0.7026 time to fit residues: 241.8568 Evaluate side-chains 310 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 858 LYS Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 2 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 50 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 144 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092328 restraints weight = 38331.615| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.26 r_work: 0.3081 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24075 Z= 0.110 Angle : 0.573 12.969 32601 Z= 0.282 Chirality : 0.041 0.167 3879 Planarity : 0.004 0.046 4086 Dihedral : 5.906 55.544 3390 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.45 % Allowed : 20.93 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 3063 helix: 0.73 (0.13), residues: 1653 sheet: 0.02 (0.22), residues: 516 loop : -0.68 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 67 TYR 0.016 0.001 TYR B 883 PHE 0.013 0.001 PHE A 4 TRP 0.008 0.001 TRP C 886 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00260 (24075) covalent geometry : angle 0.57311 (32601) hydrogen bonds : bond 0.03377 ( 1132) hydrogen bonds : angle 3.82231 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8367.45 seconds wall clock time: 143 minutes 0.59 seconds (8580.59 seconds total)