Starting phenix.real_space_refine on Sun Sep 13 14:40:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ows_20216/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_2026/6ows_20216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ows_20216/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.93, per 1000 atoms: 0.17 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: 1.54 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: 0.91 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: 5.23 Time building geometry restraints manager: 2.10 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: 13642 24.86 - 49.72: 836 49.72 - 74.58: 102 74.58 - 99.43: 12 99.43 - 124.29: 3 Dihedral angle restraints: 14595 sinusoidal: 5754 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 14592 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.560 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 15.558 124.293 8877 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/Z covalent geometry : bond 0.00900 / 0.45 (24075) covalent geometry : angle 1.04246 / 0.56 (32601) hydrogen bonds : bond 0.32282 / 21.32 ( 1132) hydrogen bonds : angle 9.67988 / 6.72 ( 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 : 0.671 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: 0.5666 time to fit residues: 419.1150 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 : 0.907 ------------------------------------------------------------------------------- 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... 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 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 717 ASN B 779 ASN B 805 GLN 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092656 restraints weight = 38738.164| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.21 r_work: 0.3084 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24075 Z= 0.151 Angle : 0.656 10.564 32601 Z= 0.337 Chirality : 0.043 0.163 3879 Planarity : 0.006 0.070 4086 Dihedral : 9.015 115.032 3415 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.42 % Allowed : 15.87 % Favored : 80.71 % 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: -3.39 (0.13), residues: 3063 helix: -2.40 (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 0.013 0.001 TYR B 883 PHE 0.024 0.002 PHE B 824 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (24075) covalent geometry : angle 0.65640 / 0.34 (32601) hydrogen bonds : bond 0.05641 / 3.73 ( 1132) hydrogen bonds : angle 4.85376 / 3.35 ( 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 426 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 338 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.9204 (mt0) cc_final: 0.8887 (mt0) REVERT: A 89 GLU cc_start: 0.8334 (tt0) cc_final: 0.7971 (tp30) REVERT: A 128 GLN cc_start: 0.7919 (mp10) cc_final: 0.7501 (mp10) REVERT: A 357 LEU cc_start: 0.8182 (mm) cc_final: 0.7943 (tt) REVERT: A 525 GLU cc_start: 0.8302 (tt0) cc_final: 0.7719 (tp30) REVERT: A 529 LEU cc_start: 0.8637 (tp) cc_final: 0.8300 (mm) REVERT: A 590 GLN cc_start: 0.8314 (tp40) cc_final: 0.7578 (tp-100) REVERT: A 637 SER cc_start: 0.8646 (t) cc_final: 0.8340 (m) REVERT: A 649 ASN cc_start: 0.8559 (m110) cc_final: 0.8041 (p0) REVERT: A 656 MET cc_start: 0.8695 (tpt) cc_final: 0.8429 (tpt) REVERT: A 706 MET cc_start: 0.7070 (mtp) cc_final: 0.5832 (tpt) REVERT: A 783 MET cc_start: 0.9353 (tpt) cc_final: 0.9113 (tpp) REVERT: A 844 LYS cc_start: 0.8791 (tttm) cc_final: 0.8125 (mppt) REVERT: A 849 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8613 (mt-10) REVERT: A 864 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7245 (tpp) REVERT: A 893 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8409 (mmp) REVERT: A 938 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: A 963 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: A 970 LEU cc_start: 0.8174 (pp) cc_final: 0.7826 (mt) REVERT: B 1 MET cc_start: 0.5132 (mmm) cc_final: 0.4077 (mpp) REVERT: B 112 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8263 (ptpt) REVERT: B 128 GLN cc_start: 0.7804 (mp10) cc_final: 0.7444 (mp10) REVERT: B 138 MET cc_start: 0.8854 (ptm) cc_final: 0.8649 (ptm) REVERT: B 184 MET cc_start: 0.9367 (tpp) cc_final: 0.9055 (tpp) REVERT: B 235 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8564 (m) REVERT: B 292 GLN cc_start: 0.8643 (mt0) cc_final: 0.8338 (mt0) REVERT: B 525 GLU cc_start: 0.8379 (tt0) cc_final: 0.7967 (tp30) REVERT: B 529 LEU cc_start: 0.8544 (mt) cc_final: 0.8297 (mm) REVERT: B 538 MET cc_start: 0.7071 (mmm) cc_final: 0.6714 (mtp) REVERT: B 553 MET cc_start: 0.8501 (mtp) cc_final: 0.8031 (mmp) REVERT: B 590 GLN cc_start: 0.8326 (tp40) cc_final: 0.7737 (tp-100) REVERT: B 637 SER cc_start: 0.8676 (t) cc_final: 0.8369 (m) REVERT: B 706 MET cc_start: 0.6606 (ttt) cc_final: 0.6138 (mtp) REVERT: B 745 MET cc_start: 0.8496 (mtm) cc_final: 0.8199 (mtm) REVERT: B 824 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6937 (p90) REVERT: B 844 LYS cc_start: 0.9033 (tttm) cc_final: 0.8352 (mmpt) REVERT: B 904 ILE cc_start: 0.8431 (pt) cc_final: 0.8188 (pp) REVERT: B 952 GLU cc_start: 0.8605 (mp0) cc_final: 0.8397 (mp0) REVERT: C 7 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7497 (ptt90) REVERT: C 112 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8014 (ptpt) REVERT: C 128 GLN cc_start: 0.7796 (mp10) cc_final: 0.7589 (mp10) REVERT: C 292 GLN cc_start: 0.8716 (mt0) cc_final: 0.8415 (mt0) REVERT: C 321 MET cc_start: 0.9001 (mtt) cc_final: 0.8659 (mtt) REVERT: C 355 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: C 420 MET cc_start: 0.8412 (mtm) cc_final: 0.8195 (mtp) REVERT: C 449 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8485 (mp) REVERT: C 487 ILE cc_start: 0.8027 (mt) cc_final: 0.7794 (mt) REVERT: C 538 MET cc_start: 0.7056 (mmm) cc_final: 0.6540 (ttp) REVERT: C 564 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7612 (mm-30) REVERT: C 783 MET cc_start: 0.9373 (tpt) cc_final: 0.9143 (tpp) REVERT: C 824 PHE cc_start: 0.7261 (t80) cc_final: 0.7049 (t80) REVERT: C 835 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8661 (mmm) REVERT: C 844 LYS cc_start: 0.8969 (tttm) cc_final: 0.8186 (mmmt) REVERT: C 864 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: C 942 MET cc_start: 0.8255 (ttm) cc_final: 0.7766 (tmt) REVERT: C 952 GLU cc_start: 0.8447 (mp0) cc_final: 0.8154 (mp0) outliers start: 88 outliers final: 23 residues processed: 394 average time/residue: 0.6123 time to fit residues: 275.8825 Evaluate side-chains 310 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU 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 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 SER 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 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 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 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: 0.8980 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 270 optimal weight: 0.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN B 604 ASN B 788 GLN B 863 GLN C 120 GLN C 788 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093304 restraints weight = 38599.933| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.10 r_work: 0.3081 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3281 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= 0.133 Angle : 0.591 10.353 32601 Z= 0.301 Chirality : 0.042 0.155 3879 Planarity : 0.005 0.056 4086 Dihedral : 7.403 88.447 3368 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.77 % Allowed : 16.88 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.14), residues: 3063 helix: -1.08 (0.12), residues: 1617 sheet: -1.36 (0.20), residues: 540 loop : -1.22 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 67 TYR 0.010 0.001 TYR B 883 PHE 0.021 0.001 PHE A 4 TRP 0.006 0.001 TRP C 512 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (24075) covalent geometry : angle 0.59141 / 0.30 (32601) hydrogen bonds : bond 0.04590 / 3.03 ( 1132) hydrogen bonds : angle 4.25859 / 2.92 ( 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 392 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 295 time to evaluate : 0.789 Fit side-chains REVERT: A 1 MET cc_start: 0.5417 (mmm) cc_final: 0.4900 (mpp) REVERT: A 42 GLN cc_start: 0.9211 (mt0) cc_final: 0.8932 (mt0) REVERT: A 89 GLU cc_start: 0.8379 (tt0) cc_final: 0.8012 (tp30) REVERT: A 128 GLN cc_start: 0.7912 (mp10) cc_final: 0.7638 (mp10) REVERT: A 164 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8027 (pm20) REVERT: A 292 GLN cc_start: 0.8787 (mt0) cc_final: 0.8338 (mt0) REVERT: A 338 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: A 425 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5620 (tp) REVERT: A 525 GLU cc_start: 0.8266 (tt0) cc_final: 0.7878 (mm-30) REVERT: A 529 LEU cc_start: 0.8629 (tp) cc_final: 0.8275 (mm) REVERT: A 590 GLN cc_start: 0.8288 (tp40) cc_final: 0.7789 (mt0) REVERT: A 649 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7985 (p0) REVERT: A 783 MET cc_start: 0.9374 (tpt) cc_final: 0.9107 (tpp) REVERT: A 824 PHE cc_start: 0.7093 (t80) cc_final: 0.6762 (p90) REVERT: A 844 LYS cc_start: 0.8785 (tttm) cc_final: 0.8338 (mmpt) REVERT: A 849 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 864 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7271 (tpp) REVERT: A 893 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7993 (mpm) REVERT: A 938 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: B 1 MET cc_start: 0.5301 (mmm) cc_final: 0.4197 (mpp) REVERT: B 68 GLU cc_start: 0.8140 (mp0) cc_final: 0.7715 (mp0) REVERT: B 120 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (mm110) REVERT: B 128 GLN cc_start: 0.7912 (mp10) cc_final: 0.7581 (mp10) REVERT: B 221 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: B 235 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (m) REVERT: B 292 GLN cc_start: 0.8597 (mt0) cc_final: 0.8324 (mt0) REVERT: B 398 MET cc_start: 0.8437 (mmm) cc_final: 0.7843 (mmm) REVERT: B 425 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5452 (tp) REVERT: B 538 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7124 (mtp) REVERT: B 553 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8100 (mmp) REVERT: B 590 GLN cc_start: 0.8471 (tp40) cc_final: 0.7901 (mt0) REVERT: B 633 THR cc_start: 0.7456 (p) cc_final: 0.7220 (t) REVERT: B 637 SER cc_start: 0.8739 (t) cc_final: 0.8372 (m) REVERT: B 706 MET cc_start: 0.6660 (ttt) cc_final: 0.6216 (mtp) REVERT: B 745 MET cc_start: 0.8597 (mtm) cc_final: 0.8364 (mtm) REVERT: B 844 LYS cc_start: 0.8913 (tttm) cc_final: 0.8340 (mmpt) REVERT: C 1 MET cc_start: 0.5352 (mmm) cc_final: 0.5145 (mmm) REVERT: C 7 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7483 (ptt90) REVERT: C 134 SER cc_start: 0.8325 (m) cc_final: 0.8063 (p) REVERT: C 164 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8071 (pm20) REVERT: C 292 GLN cc_start: 0.8720 (mt0) cc_final: 0.8424 (mt0) REVERT: C 420 MET cc_start: 0.8598 (mtm) cc_final: 0.8370 (mtp) REVERT: C 425 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5718 (tp) REVERT: C 449 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 512 TRP cc_start: 0.7510 (t60) cc_final: 0.7232 (t60) REVERT: C 538 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6919 (mtp) REVERT: C 564 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7640 (mm-30) REVERT: C 633 THR cc_start: 0.7645 (p) cc_final: 0.7406 (t) REVERT: C 637 SER cc_start: 0.8563 (t) cc_final: 0.8212 (m) REVERT: C 783 MET cc_start: 0.9354 (tpt) cc_final: 0.9125 (tpp) REVERT: C 824 PHE cc_start: 0.7270 (t80) cc_final: 0.7060 (t80) REVERT: C 835 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: C 844 LYS cc_start: 0.8950 (tttm) cc_final: 0.8207 (mmmt) REVERT: C 861 GLU cc_start: 0.8572 (tp30) cc_final: 0.8123 (tt0) REVERT: C 864 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7300 (tpp) REVERT: C 942 MET cc_start: 0.8316 (ttm) cc_final: 0.7798 (tmt) REVERT: C 943 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7730 (mp) REVERT: C 997 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8329 (m) outliers start: 97 outliers final: 28 residues processed: 363 average time/residue: 0.6089 time to fit residues: 252.8994 Evaluate side-chains 317 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 269 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 338 GLU 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 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 538 MET Chi-restraints excluded: chain B residue 553 MET 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 199 SER 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 483 LEU 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 997 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 129 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 220 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN B 292 GLN B 717 ASN B 805 GLN B 859 GLN C 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092006 restraints weight = 38494.109| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.22 r_work: 0.3071 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3560 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= 0.126 Angle : 0.571 10.992 32601 Z= 0.288 Chirality : 0.041 0.204 3879 Planarity : 0.004 0.049 4086 Dihedral : 6.931 73.155 3365 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.85 % Allowed : 17.00 % Favored : 79.15 % 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: -1.21 (0.15), residues: 3063 helix: -0.42 (0.13), residues: 1623 sheet: -0.88 (0.21), residues: 510 loop : -1.11 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.011 0.001 TYR B 883 PHE 0.024 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/Z covalent geometry : bond 0.00298 / 0.13 (24075) covalent geometry : angle 0.57107 / 0.29 (32601) hydrogen bonds : bond 0.04063 / 2.69 ( 1132) hydrogen bonds : angle 4.09254 / 2.81 ( 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 388 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 289 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5579 (mmm) cc_final: 0.5097 (mpp) REVERT: A 42 GLN cc_start: 0.9303 (mt0) cc_final: 0.8893 (mt0) REVERT: A 89 GLU cc_start: 0.8423 (tt0) cc_final: 0.8046 (tp30) REVERT: A 128 GLN cc_start: 0.7908 (mp10) cc_final: 0.7641 (mp10) REVERT: A 292 GLN cc_start: 0.8819 (mt0) cc_final: 0.8286 (mt0) REVERT: A 338 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 425 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5515 (tp) REVERT: A 525 GLU cc_start: 0.8277 (tt0) cc_final: 0.7853 (mm-30) REVERT: A 529 LEU cc_start: 0.8596 (tp) cc_final: 0.8183 (mm) REVERT: A 590 GLN cc_start: 0.8230 (tp40) cc_final: 0.7747 (tt0) REVERT: A 637 SER cc_start: 0.8643 (t) cc_final: 0.8293 (m) REVERT: A 639 MET cc_start: 0.8356 (mtm) cc_final: 0.8051 (mtm) REVERT: A 649 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 706 MET cc_start: 0.7171 (mtp) cc_final: 0.6079 (tpp) REVERT: A 783 MET cc_start: 0.9370 (tpt) cc_final: 0.9091 (tpp) REVERT: A 824 PHE cc_start: 0.7080 (t80) cc_final: 0.6847 (p90) REVERT: A 844 LYS cc_start: 0.8786 (tttm) cc_final: 0.8179 (mppt) REVERT: A 849 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8653 (mt-10) REVERT: A 864 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: A 938 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: B 1 MET cc_start: 0.5454 (mmm) cc_final: 0.4359 (mpp) REVERT: B 68 GLU cc_start: 0.8137 (mp0) cc_final: 0.7721 (mp0) REVERT: B 112 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (mttt) REVERT: B 128 GLN cc_start: 0.7840 (mp10) cc_final: 0.7471 (mp10) REVERT: B 134 SER cc_start: 0.8401 (m) cc_final: 0.8167 (p) REVERT: B 221 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: B 235 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 292 GLN cc_start: 0.8525 (mt0) cc_final: 0.8260 (mt0) REVERT: B 395 MET cc_start: 0.8381 (mmm) cc_final: 0.8145 (mmp) REVERT: B 398 MET cc_start: 0.8356 (mmm) cc_final: 0.7847 (mmm) REVERT: B 402 ILE cc_start: 0.8849 (mm) cc_final: 0.8640 (tp) REVERT: B 425 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5349 (tp) REVERT: B 529 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7841 (mm) REVERT: B 553 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8064 (mmp) REVERT: B 590 GLN cc_start: 0.8374 (tp40) cc_final: 0.7834 (mt0) REVERT: B 633 THR cc_start: 0.7410 (p) cc_final: 0.7206 (t) REVERT: B 637 SER cc_start: 0.8698 (t) cc_final: 0.8336 (m) REVERT: B 706 MET cc_start: 0.6680 (ttt) cc_final: 0.6215 (mtp) REVERT: B 844 LYS cc_start: 0.8953 (tttm) cc_final: 0.8406 (mmpt) REVERT: B 952 GLU cc_start: 0.8656 (mp0) cc_final: 0.8421 (mp0) REVERT: C 1 MET cc_start: 0.5523 (mmm) cc_final: 0.5320 (mmm) REVERT: C 7 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7438 (ptt90) REVERT: C 73 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8740 (ptpp) REVERT: C 95 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8701 (mtmm) REVERT: C 134 SER cc_start: 0.8364 (m) cc_final: 0.8115 (p) REVERT: C 164 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8084 (pm20) REVERT: C 229 LEU cc_start: 0.8257 (mt) cc_final: 0.7709 (mp) REVERT: C 292 GLN cc_start: 0.8726 (mt0) cc_final: 0.8434 (mt0) REVERT: C 425 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5601 (tp) REVERT: C 449 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 512 TRP cc_start: 0.7534 (t60) cc_final: 0.7309 (t60) REVERT: C 538 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6934 (mtp) REVERT: C 633 THR cc_start: 0.7613 (p) cc_final: 0.7394 (t) REVERT: C 637 SER cc_start: 0.8479 (t) cc_final: 0.8115 (m) REVERT: C 783 MET cc_start: 0.9372 (tpt) cc_final: 0.9141 (tpp) REVERT: C 824 PHE cc_start: 0.7305 (t80) cc_final: 0.7061 (t80) REVERT: C 835 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8668 (mmm) REVERT: C 844 LYS cc_start: 0.8912 (tttm) cc_final: 0.8194 (mmmt) REVERT: C 861 GLU cc_start: 0.8600 (tp30) cc_final: 0.8195 (tt0) REVERT: C 864 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7306 (tpp) REVERT: C 908 MET cc_start: 0.8743 (mtt) cc_final: 0.8540 (mtt) REVERT: C 942 MET cc_start: 0.8284 (ttm) cc_final: 0.7758 (tmt) REVERT: C 943 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7620 (mp) REVERT: C 997 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8274 (m) outliers start: 99 outliers final: 36 residues processed: 355 average time/residue: 0.5933 time to fit residues: 241.8467 Evaluate side-chains 323 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 338 GLU 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 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 112 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 226 LYS 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 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 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 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 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 673 SER 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 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: 1.9990 chunk 10 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 304 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN C 120 GLN C 717 ASN C 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092079 restraints weight = 38437.719| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.16 r_work: 0.3081 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3764 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= 0.124 Angle : 0.566 11.493 32601 Z= 0.283 Chirality : 0.041 0.151 3879 Planarity : 0.004 0.046 4086 Dihedral : 6.604 63.424 3364 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.66 % Allowed : 17.81 % Favored : 78.53 % 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: -0.80 (0.15), residues: 3063 helix: -0.02 (0.13), residues: 1617 sheet: -0.78 (0.21), residues: 546 loop : -1.01 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.013 0.001 TYR C 883 PHE 0.017 0.001 PHE A 824 TRP 0.004 0.001 TRP B 512 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (24075) covalent geometry : angle 0.56626 / 0.28 (32601) hydrogen bonds : bond 0.03852 / 2.54 ( 1132) hydrogen bonds : angle 3.98156 / 2.73 ( 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 370 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5584 (mmm) cc_final: 0.5059 (mpp) REVERT: A 89 GLU cc_start: 0.8439 (tt0) cc_final: 0.8058 (tp30) REVERT: A 128 GLN cc_start: 0.7869 (mp10) cc_final: 0.7608 (mp10) REVERT: A 165 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8081 (pp20) REVERT: A 292 GLN cc_start: 0.8791 (mt0) cc_final: 0.8278 (mt0) REVERT: A 338 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: A 425 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5365 (tp) REVERT: A 525 GLU cc_start: 0.8285 (tt0) cc_final: 0.7898 (mm-30) REVERT: A 529 LEU cc_start: 0.8615 (tp) cc_final: 0.8173 (mm) REVERT: A 590 GLN cc_start: 0.8270 (tp40) cc_final: 0.7736 (tt0) REVERT: A 637 SER cc_start: 0.8647 (t) cc_final: 0.8276 (m) REVERT: A 639 MET cc_start: 0.8339 (mtm) cc_final: 0.8056 (mtm) REVERT: A 649 ASN cc_start: 0.8483 (m110) cc_final: 0.7842 (p0) REVERT: A 706 MET cc_start: 0.7154 (mtp) cc_final: 0.5690 (tpt) REVERT: A 783 MET cc_start: 0.9380 (tpt) cc_final: 0.9099 (tpp) REVERT: A 844 LYS cc_start: 0.8823 (tttm) cc_final: 0.8147 (mppt) REVERT: A 849 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 864 MET cc_start: 0.8161 (ttm) cc_final: 0.7068 (tpp) REVERT: A 888 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7213 (tt) REVERT: A 938 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: A 961 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7687 (mtt180) REVERT: B 1 MET cc_start: 0.5639 (mmm) cc_final: 0.4530 (mpp) REVERT: B 67 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8090 (ptm-80) REVERT: B 68 GLU cc_start: 0.8153 (mp0) cc_final: 0.7568 (mp0) REVERT: B 128 GLN cc_start: 0.7798 (mp10) cc_final: 0.7442 (mp10) REVERT: B 134 SER cc_start: 0.8410 (m) cc_final: 0.8191 (p) REVERT: B 221 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: B 292 GLN cc_start: 0.8465 (mt0) cc_final: 0.8213 (mt0) REVERT: B 398 MET cc_start: 0.8270 (mmm) cc_final: 0.7824 (mmm) REVERT: B 425 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5638 (tt) REVERT: B 483 LEU cc_start: 0.8376 (pp) cc_final: 0.8086 (tt) REVERT: B 529 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7864 (mm) REVERT: B 553 MET cc_start: 0.8463 (mtp) cc_final: 0.8099 (mmp) REVERT: B 633 THR cc_start: 0.7358 (p) cc_final: 0.7141 (t) REVERT: B 637 SER cc_start: 0.8660 (t) cc_final: 0.8290 (m) REVERT: B 706 MET cc_start: 0.6715 (ttt) cc_final: 0.6255 (mtp) REVERT: B 844 LYS cc_start: 0.8904 (tttm) cc_final: 0.8372 (mmpt) REVERT: B 888 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7160 (tt) REVERT: C 1 MET cc_start: 0.5688 (mmm) cc_final: 0.5321 (mmm) REVERT: C 7 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7459 (ptt90) REVERT: C 73 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (ptpp) REVERT: C 164 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8031 (pm20) REVERT: C 229 LEU cc_start: 0.8228 (mt) cc_final: 0.8008 (mm) REVERT: C 292 GLN cc_start: 0.8690 (mt0) cc_final: 0.8389 (mt0) REVERT: C 425 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5521 (tp) REVERT: C 449 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8687 (tp) REVERT: C 512 TRP cc_start: 0.7567 (t60) cc_final: 0.7315 (t60) REVERT: C 538 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6859 (mtp) REVERT: C 633 THR cc_start: 0.7542 (p) cc_final: 0.7319 (t) REVERT: C 637 SER cc_start: 0.8355 (t) cc_final: 0.7983 (m) REVERT: C 639 MET cc_start: 0.8206 (mtm) cc_final: 0.7973 (mtm) REVERT: C 706 MET cc_start: 0.7522 (mtp) cc_final: 0.6093 (tpt) REVERT: C 783 MET cc_start: 0.9365 (tpt) cc_final: 0.9140 (tpp) REVERT: C 824 PHE cc_start: 0.7283 (t80) cc_final: 0.7045 (p90) REVERT: C 835 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: C 844 LYS cc_start: 0.8908 (tttm) cc_final: 0.8184 (mmmt) REVERT: C 864 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7171 (tpp) REVERT: C 907 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7300 (mm) REVERT: C 913 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7002 (mpp) REVERT: C 942 MET cc_start: 0.8259 (ttm) cc_final: 0.7729 (tmt) REVERT: C 943 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mp) REVERT: C 970 LEU cc_start: 0.8234 (pp) cc_final: 0.8006 (mt) REVERT: C 997 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (m) outliers start: 94 outliers final: 39 residues processed: 345 average time/residue: 0.6027 time to fit residues: 239.1539 Evaluate side-chains 319 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 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 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 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 199 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 345 LEU 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 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 C residue 7 ARG 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 529 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 262 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 219 optimal weight: 0.2980 chunk 254 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3576 r_free = 0.3576 target = 0.117488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091814 restraints weight = 38602.714| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.22 r_work: 0.3069 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3928 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= 0.123 Angle : 0.563 11.593 32601 Z= 0.281 Chirality : 0.041 0.136 3879 Planarity : 0.004 0.043 4086 Dihedral : 6.248 59.434 3359 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.38 % Allowed : 18.24 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3063 helix: 0.20 (0.13), residues: 1629 sheet: -0.58 (0.21), residues: 546 loop : -0.93 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 168 TYR 0.011 0.001 TYR B 883 PHE 0.014 0.001 PHE A 4 TRP 0.004 0.001 TRP B 512 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (24075) covalent geometry : angle 0.56324 / 0.28 (32601) hydrogen bonds : bond 0.03748 / 2.47 ( 1132) hydrogen bonds : angle 3.92173 / 2.69 ( 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 359 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 272 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5840 (mmm) cc_final: 0.5347 (mpp) REVERT: A 89 GLU cc_start: 0.8443 (tt0) cc_final: 0.8102 (tp30) REVERT: A 120 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8476 (mm110) REVERT: A 128 GLN cc_start: 0.7909 (mp10) cc_final: 0.7644 (mp10) REVERT: A 165 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: A 292 GLN cc_start: 0.8819 (mt0) cc_final: 0.8278 (mt0) REVERT: A 338 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 425 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5378 (tp) REVERT: A 525 GLU cc_start: 0.8261 (tt0) cc_final: 0.8025 (mm-30) REVERT: A 529 LEU cc_start: 0.8623 (tp) cc_final: 0.8213 (mm) REVERT: A 590 GLN cc_start: 0.8262 (tp40) cc_final: 0.7757 (tt0) REVERT: A 633 THR cc_start: 0.7423 (p) cc_final: 0.7149 (t) REVERT: A 637 SER cc_start: 0.8495 (t) cc_final: 0.8097 (m) REVERT: A 639 MET cc_start: 0.8378 (mtm) cc_final: 0.8070 (mtm) REVERT: A 649 ASN cc_start: 0.8383 (m110) cc_final: 0.7759 (p0) REVERT: A 656 MET cc_start: 0.8548 (tpt) cc_final: 0.8196 (mmt) REVERT: A 783 MET cc_start: 0.9394 (tpt) cc_final: 0.9122 (tpp) REVERT: A 844 LYS cc_start: 0.8772 (tttm) cc_final: 0.8100 (mppt) REVERT: A 849 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8655 (mt-10) REVERT: A 864 MET cc_start: 0.8178 (ttm) cc_final: 0.7062 (tpp) REVERT: A 938 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: A 961 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7592 (mtt180) REVERT: B 1 MET cc_start: 0.5778 (mmm) cc_final: 0.5424 (mmm) REVERT: B 4 PHE cc_start: 0.8407 (t80) cc_final: 0.8061 (t80) REVERT: B 67 ARG cc_start: 0.8648 (ptm-80) cc_final: 0.8063 (ptm-80) REVERT: B 68 GLU cc_start: 0.8183 (mp0) cc_final: 0.7571 (mp0) REVERT: B 99 ASP cc_start: 0.8852 (t0) cc_final: 0.8606 (t0) REVERT: B 128 GLN cc_start: 0.7849 (mp10) cc_final: 0.7513 (mp10) REVERT: B 134 SER cc_start: 0.8455 (m) cc_final: 0.8198 (p) REVERT: B 292 GLN cc_start: 0.8492 (mt0) cc_final: 0.8196 (mt0) REVERT: B 425 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5778 (tt) REVERT: B 529 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7885 (mm) REVERT: B 553 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (mmp) REVERT: B 633 THR cc_start: 0.7411 (p) cc_final: 0.7189 (t) REVERT: B 637 SER cc_start: 0.8685 (t) cc_final: 0.8314 (m) REVERT: B 706 MET cc_start: 0.6778 (ttt) cc_final: 0.6351 (mtp) REVERT: B 844 LYS cc_start: 0.8859 (tttm) cc_final: 0.8346 (mmpt) REVERT: B 888 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7169 (tt) REVERT: B 952 GLU cc_start: 0.8754 (mp0) cc_final: 0.8456 (mp0) REVERT: C 1 MET cc_start: 0.5731 (mmm) cc_final: 0.5361 (mmm) REVERT: C 7 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7441 (ptt90) REVERT: C 73 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8808 (ptpp) REVERT: C 102 MET cc_start: 0.7821 (mmt) cc_final: 0.7225 (mmm) REVERT: C 164 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8012 (pm20) REVERT: C 168 ARG cc_start: 0.8280 (mmt90) cc_final: 0.8036 (mmt90) REVERT: C 292 GLN cc_start: 0.8663 (mt0) cc_final: 0.8366 (mt0) REVERT: C 425 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5539 (tp) REVERT: C 449 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 512 TRP cc_start: 0.7630 (t60) cc_final: 0.7405 (t60) REVERT: C 538 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6902 (mtp) REVERT: C 539 MET cc_start: 0.7849 (tpt) cc_final: 0.7532 (mmt) REVERT: C 633 THR cc_start: 0.7428 (p) cc_final: 0.7205 (t) REVERT: C 637 SER cc_start: 0.8399 (t) cc_final: 0.8007 (m) REVERT: C 639 MET cc_start: 0.8195 (mtm) cc_final: 0.7981 (mtm) REVERT: C 706 MET cc_start: 0.7247 (mtp) cc_final: 0.5848 (tpt) REVERT: C 783 MET cc_start: 0.9394 (tpt) cc_final: 0.9171 (tpp) REVERT: C 824 PHE cc_start: 0.7290 (t80) cc_final: 0.7039 (p90) REVERT: C 835 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8573 (mmm) REVERT: C 844 LYS cc_start: 0.8957 (tttm) cc_final: 0.8213 (mmmt) REVERT: C 861 GLU cc_start: 0.8525 (tp30) cc_final: 0.8002 (tt0) REVERT: C 864 MET cc_start: 0.8256 (ttm) cc_final: 0.7112 (tpp) REVERT: C 907 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7364 (mm) REVERT: C 942 MET cc_start: 0.8207 (ttm) cc_final: 0.7727 (tmt) REVERT: C 943 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7554 (mp) REVERT: C 970 LEU cc_start: 0.8251 (pp) cc_final: 0.8048 (mt) REVERT: C 997 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8293 (m) outliers start: 87 outliers final: 37 residues processed: 333 average time/residue: 0.6174 time to fit residues: 236.1797 Evaluate side-chains 306 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 19 ILE 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 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 744 SER 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 199 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 544 VAL 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 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain C residue 7 ARG 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 186 optimal weight: 0.0770 chunk 97 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 230 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 534 HIS 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 = 0.3582 r_free = 0.3582 target = 0.117981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093240 restraints weight = 38404.154| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4044 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= 0.117 Angle : 0.566 12.203 32601 Z= 0.281 Chirality : 0.041 0.191 3879 Planarity : 0.004 0.042 4086 Dihedral : 6.015 54.886 3356 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.19 % Allowed : 19.02 % 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: -0.28 (0.15), residues: 3063 helix: 0.38 (0.13), residues: 1635 sheet: -0.42 (0.22), residues: 546 loop : -0.84 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 168 TYR 0.013 0.001 TYR B 883 PHE 0.013 0.001 PHE A 824 TRP 0.004 0.001 TRP C 886 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24075) covalent geometry : angle 0.56589 / 0.28 (32601) hydrogen bonds : bond 0.03613 / 2.37 ( 1132) hydrogen bonds : angle 3.88625 / 2.67 ( 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: 82 poor density : 261 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5904 (mmm) cc_final: 0.5426 (mpp) REVERT: A 89 GLU cc_start: 0.8390 (tt0) cc_final: 0.8070 (tp30) REVERT: A 120 GLN cc_start: 0.8717 (mp-120) cc_final: 0.8430 (mm110) REVERT: A 128 GLN cc_start: 0.7902 (mp10) cc_final: 0.7642 (mp10) REVERT: A 134 SER cc_start: 0.8459 (m) cc_final: 0.8251 (p) REVERT: A 165 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (pp20) REVERT: A 338 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 425 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5339 (tp) REVERT: A 525 GLU cc_start: 0.8210 (tt0) cc_final: 0.8006 (mm-30) REVERT: A 529 LEU cc_start: 0.8666 (tp) cc_final: 0.8315 (mm) REVERT: A 590 GLN cc_start: 0.8261 (tp40) cc_final: 0.7785 (tt0) REVERT: A 637 SER cc_start: 0.8481 (t) cc_final: 0.8080 (m) REVERT: A 649 ASN cc_start: 0.8343 (m110) cc_final: 0.7685 (p0) REVERT: A 706 MET cc_start: 0.7142 (mtp) cc_final: 0.5791 (tpt) REVERT: A 783 MET cc_start: 0.9386 (tpt) cc_final: 0.9132 (tpp) REVERT: A 844 LYS cc_start: 0.8779 (tttm) cc_final: 0.8115 (mppt) REVERT: A 849 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8615 (mt-10) REVERT: A 864 MET cc_start: 0.8127 (ttm) cc_final: 0.7011 (tpp) REVERT: A 888 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7248 (tt) REVERT: A 938 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: A 961 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7648 (mtt180) REVERT: B 1 MET cc_start: 0.5880 (mmm) cc_final: 0.5535 (mmm) REVERT: B 4 PHE cc_start: 0.8412 (t80) cc_final: 0.8093 (t80) REVERT: B 67 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8183 (ptm-80) REVERT: B 68 GLU cc_start: 0.8182 (mp0) cc_final: 0.7596 (mp0) REVERT: B 99 ASP cc_start: 0.8923 (t0) cc_final: 0.8672 (t0) REVERT: B 128 GLN cc_start: 0.7850 (mp10) cc_final: 0.7520 (mp10) REVERT: B 134 SER cc_start: 0.8416 (m) cc_final: 0.8157 (p) REVERT: B 292 GLN cc_start: 0.8483 (mt0) cc_final: 0.8222 (mt0) REVERT: B 353 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8123 (mp) REVERT: B 398 MET cc_start: 0.8408 (mmm) cc_final: 0.7927 (mmm) REVERT: B 425 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5803 (tt) REVERT: B 529 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7944 (mm) REVERT: B 553 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8113 (mmp) REVERT: B 633 THR cc_start: 0.7390 (p) cc_final: 0.7175 (t) REVERT: B 637 SER cc_start: 0.8692 (t) cc_final: 0.8335 (m) REVERT: B 706 MET cc_start: 0.6681 (ttt) cc_final: 0.6262 (mtp) REVERT: B 844 LYS cc_start: 0.8844 (tttm) cc_final: 0.8354 (mmpt) REVERT: B 888 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7194 (tt) REVERT: B 893 MET cc_start: 0.8662 (mmp) cc_final: 0.8419 (mmp) REVERT: C 1 MET cc_start: 0.5936 (mmm) cc_final: 0.5565 (mmm) REVERT: C 7 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7465 (ptt90) REVERT: C 73 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8808 (ptpp) REVERT: C 102 MET cc_start: 0.7628 (mmt) cc_final: 0.7051 (mmm) REVERT: C 164 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8126 (pt0) REVERT: C 165 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8014 (pp20) REVERT: C 168 ARG cc_start: 0.8378 (mmt90) cc_final: 0.8120 (mmt90) REVERT: C 292 GLN cc_start: 0.8651 (mt0) cc_final: 0.8364 (mt0) REVERT: C 425 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5713 (tp) REVERT: C 449 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8778 (tp) REVERT: C 512 TRP cc_start: 0.7658 (t60) cc_final: 0.7417 (t60) REVERT: C 538 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6877 (mtp) REVERT: C 539 MET cc_start: 0.7824 (tpt) cc_final: 0.7528 (mmt) REVERT: C 633 THR cc_start: 0.7466 (p) cc_final: 0.7232 (t) REVERT: C 637 SER cc_start: 0.8415 (t) cc_final: 0.8022 (m) REVERT: C 706 MET cc_start: 0.7209 (mtp) cc_final: 0.5844 (tpt) REVERT: C 783 MET cc_start: 0.9375 (tpt) cc_final: 0.9161 (tpp) REVERT: C 835 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8618 (mmm) REVERT: C 844 LYS cc_start: 0.8937 (tttm) cc_final: 0.8352 (mmpt) REVERT: C 861 GLU cc_start: 0.8572 (tp30) cc_final: 0.8048 (tt0) REVERT: C 864 MET cc_start: 0.8189 (ttm) cc_final: 0.7096 (tpp) REVERT: C 907 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7413 (mm) REVERT: C 942 MET cc_start: 0.8225 (ttm) cc_final: 0.7758 (tmt) REVERT: C 943 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7591 (mp) REVERT: C 997 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8314 (m) outliers start: 82 outliers final: 37 residues processed: 325 average time/residue: 0.6101 time to fit residues: 227.9081 Evaluate side-chains 308 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 338 GLU 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 630 LYS 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 194 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 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 536 VAL 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 888 ILE Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 LYS 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 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 544 VAL 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 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 909 SER 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: 0.6980 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 225 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN B 120 GLN B 534 HIS C 120 GLN C 604 ASN C 691 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091036 restraints weight = 38369.011| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.21 r_work: 0.3055 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4118 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= 0.136 Angle : 0.581 12.791 32601 Z= 0.288 Chirality : 0.042 0.140 3879 Planarity : 0.004 0.041 4086 Dihedral : 5.913 58.813 3354 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.50 % Allowed : 19.10 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3063 helix: 0.45 (0.13), residues: 1638 sheet: -0.35 (0.22), residues: 546 loop : -0.80 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.014 0.001 TYR B 883 PHE 0.013 0.001 PHE C 824 TRP 0.005 0.001 TRP A 610 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (24075) covalent geometry : angle 0.58066 / 0.29 (32601) hydrogen bonds : bond 0.03814 / 2.52 ( 1132) hydrogen bonds : angle 3.93036 / 2.71 ( 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 346 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 256 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6104 (mmm) cc_final: 0.5593 (mpp) REVERT: A 89 GLU cc_start: 0.8458 (tt0) cc_final: 0.8095 (tp30) REVERT: A 101 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: A 128 GLN cc_start: 0.7889 (mp10) cc_final: 0.7623 (mp10) REVERT: A 165 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8371 (pp20) REVERT: A 338 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 525 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: A 529 LEU cc_start: 0.8637 (tp) cc_final: 0.8290 (mm) REVERT: A 590 GLN cc_start: 0.8215 (tp40) cc_final: 0.7714 (tt0) REVERT: A 637 SER cc_start: 0.8441 (t) cc_final: 0.8034 (m) REVERT: A 639 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: A 649 ASN cc_start: 0.8474 (m110) cc_final: 0.7690 (p0) REVERT: A 656 MET cc_start: 0.8398 (tpt) cc_final: 0.8173 (mmt) REVERT: A 783 MET cc_start: 0.9408 (tpt) cc_final: 0.9110 (tpp) REVERT: A 844 LYS cc_start: 0.8781 (tttm) cc_final: 0.8104 (mppt) REVERT: A 849 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 864 MET cc_start: 0.8135 (ttm) cc_final: 0.6959 (tpp) REVERT: A 888 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7174 (tt) REVERT: A 938 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: A 961 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7632 (mtt180) REVERT: B 1 MET cc_start: 0.5965 (mmm) cc_final: 0.5596 (mmm) REVERT: B 4 PHE cc_start: 0.8379 (t80) cc_final: 0.7994 (t80) REVERT: B 67 ARG cc_start: 0.8712 (ptm-80) cc_final: 0.8127 (ptm-80) REVERT: B 68 GLU cc_start: 0.8201 (mp0) cc_final: 0.7605 (mp0) REVERT: B 128 GLN cc_start: 0.7856 (mp10) cc_final: 0.7521 (mp10) REVERT: B 134 SER cc_start: 0.8464 (m) cc_final: 0.8187 (p) REVERT: B 292 GLN cc_start: 0.8490 (mt0) cc_final: 0.8194 (mt0) REVERT: B 353 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8035 (mp) REVERT: B 398 MET cc_start: 0.8340 (mmm) cc_final: 0.7886 (mmm) REVERT: B 529 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 553 MET cc_start: 0.8447 (mtp) cc_final: 0.7912 (mmm) REVERT: B 633 THR cc_start: 0.7419 (p) cc_final: 0.7190 (t) REVERT: B 637 SER cc_start: 0.8513 (t) cc_final: 0.8130 (m) REVERT: B 706 MET cc_start: 0.6853 (ttt) cc_final: 0.6373 (mtp) REVERT: B 844 LYS cc_start: 0.8852 (tttm) cc_final: 0.8352 (mmpt) REVERT: B 888 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7083 (tt) REVERT: C 1 MET cc_start: 0.5980 (mmm) cc_final: 0.5638 (mmm) REVERT: C 102 MET cc_start: 0.7706 (mmt) cc_final: 0.7226 (mmm) REVERT: C 128 GLN cc_start: 0.7880 (mt0) cc_final: 0.7639 (mp10) REVERT: C 164 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8096 (pt0) REVERT: C 165 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (pp20) REVERT: C 292 GLN cc_start: 0.8651 (mt0) cc_final: 0.8365 (mt0) REVERT: C 425 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5612 (tp) REVERT: C 449 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 512 TRP cc_start: 0.7660 (t60) cc_final: 0.7400 (t60) REVERT: C 538 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6761 (mtp) REVERT: C 539 MET cc_start: 0.7758 (tpt) cc_final: 0.7483 (mmt) REVERT: C 633 THR cc_start: 0.7424 (p) cc_final: 0.7182 (t) REVERT: C 637 SER cc_start: 0.8447 (t) cc_final: 0.8024 (m) REVERT: C 706 MET cc_start: 0.7524 (mtp) cc_final: 0.6219 (tpt) REVERT: C 783 MET cc_start: 0.9392 (tpt) cc_final: 0.9177 (tpp) REVERT: C 835 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8551 (mmm) REVERT: C 844 LYS cc_start: 0.8953 (tttm) cc_final: 0.8352 (mmpt) REVERT: C 858 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7823 (mmtt) REVERT: C 861 GLU cc_start: 0.8563 (tp30) cc_final: 0.7991 (tt0) REVERT: C 864 MET cc_start: 0.8187 (ttm) cc_final: 0.7033 (tpp) REVERT: C 942 MET cc_start: 0.8215 (ttm) cc_final: 0.7718 (tmt) REVERT: C 943 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7484 (mp) REVERT: C 997 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8303 (m) outliers start: 90 outliers final: 40 residues processed: 323 average time/residue: 0.5941 time to fit residues: 221.1434 Evaluate side-chains 308 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 101 GLU 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 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 630 LYS Chi-restraints excluded: chain A residue 639 MET 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 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 536 VAL Chi-restraints excluded: chain B residue 544 VAL 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 966 LEU 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 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 544 VAL 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 888 ILE Chi-restraints excluded: chain C residue 909 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 159 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 303 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 205 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN B 534 HIS 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 = 0.3570 r_free = 0.3570 target = 0.117318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091728 restraints weight = 38418.688| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.22 r_work: 0.3068 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4194 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= 0.124 Angle : 0.575 12.818 32601 Z= 0.285 Chirality : 0.041 0.143 3879 Planarity : 0.004 0.041 4086 Dihedral : 5.783 54.286 3354 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.68 % Allowed : 20.03 % 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: -0.03 (0.16), residues: 3063 helix: 0.57 (0.13), residues: 1635 sheet: -0.25 (0.22), residues: 546 loop : -0.75 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 168 TYR 0.016 0.001 TYR B 883 PHE 0.036 0.001 PHE C 824 TRP 0.005 0.001 TRP C 886 HIS 0.007 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (24075) covalent geometry : angle 0.57501 / 0.28 (32601) hydrogen bonds : bond 0.03636 / 2.40 ( 1132) hydrogen bonds : angle 3.89168 / 2.68 ( 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 318 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 249 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6274 (mmm) cc_final: 0.5745 (mpp) REVERT: A 89 GLU cc_start: 0.8456 (tt0) cc_final: 0.8109 (tp30) REVERT: A 101 GLU cc_start: 0.8564 (tp30) cc_final: 0.8113 (tp30) REVERT: A 120 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8430 (mm110) REVERT: A 128 GLN cc_start: 0.7914 (mp10) cc_final: 0.7635 (mp10) REVERT: A 165 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8433 (pp20) REVERT: A 338 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 355 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: A 525 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: A 529 LEU cc_start: 0.8625 (tp) cc_final: 0.8285 (mm) REVERT: A 590 GLN cc_start: 0.8254 (tp40) cc_final: 0.7750 (tt0) REVERT: A 649 ASN cc_start: 0.8434 (m110) cc_final: 0.7634 (p0) REVERT: A 706 MET cc_start: 0.7334 (mtm) cc_final: 0.5768 (tpt) REVERT: A 783 MET cc_start: 0.9412 (tpt) cc_final: 0.9119 (tpp) REVERT: A 844 LYS cc_start: 0.8761 (tttm) cc_final: 0.8103 (mppt) REVERT: A 849 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 864 MET cc_start: 0.8109 (ttm) cc_final: 0.6923 (tpp) REVERT: A 938 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: A 961 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7733 (mtt180) REVERT: B 1 MET cc_start: 0.5936 (mmm) cc_final: 0.5537 (mmm) REVERT: B 67 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8129 (ptm-80) REVERT: B 68 GLU cc_start: 0.8186 (mp0) cc_final: 0.7606 (mp0) REVERT: B 128 GLN cc_start: 0.7877 (mp10) cc_final: 0.7542 (mp10) REVERT: B 134 SER cc_start: 0.8437 (m) cc_final: 0.8172 (p) REVERT: B 292 GLN cc_start: 0.8470 (mt0) cc_final: 0.8201 (mt0) REVERT: B 353 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 398 MET cc_start: 0.8369 (mmm) cc_final: 0.7865 (mmm) REVERT: B 529 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7890 (mm) REVERT: B 553 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8084 (mmp) REVERT: B 633 THR cc_start: 0.7387 (p) cc_final: 0.7161 (t) REVERT: B 637 SER cc_start: 0.8493 (t) cc_final: 0.8120 (m) REVERT: B 706 MET cc_start: 0.6848 (ttt) cc_final: 0.6350 (mtp) REVERT: B 844 LYS cc_start: 0.8855 (tttm) cc_final: 0.8371 (mmpt) REVERT: B 888 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7091 (tt) REVERT: C 1 MET cc_start: 0.6248 (mmm) cc_final: 0.5907 (mmm) REVERT: C 102 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7139 (mmm) REVERT: C 128 GLN cc_start: 0.7886 (mt0) cc_final: 0.7640 (mp10) REVERT: C 164 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7982 (pm20) REVERT: C 165 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (pp20) REVERT: C 256 ASN cc_start: 0.8041 (p0) cc_final: 0.7806 (p0) REVERT: C 292 GLN cc_start: 0.8648 (mt0) cc_final: 0.8370 (mt0) REVERT: C 425 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.5700 (tp) REVERT: C 449 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8769 (tp) REVERT: C 512 TRP cc_start: 0.7670 (t60) cc_final: 0.7392 (t60) REVERT: C 538 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6805 (mtp) REVERT: C 539 MET cc_start: 0.7789 (tpt) cc_final: 0.7522 (mmt) REVERT: C 633 THR cc_start: 0.7526 (p) cc_final: 0.7270 (t) REVERT: C 637 SER cc_start: 0.8480 (t) cc_final: 0.8063 (m) REVERT: C 706 MET cc_start: 0.7422 (mtp) cc_final: 0.6109 (tpt) REVERT: C 783 MET cc_start: 0.9398 (tpt) cc_final: 0.9186 (tpp) REVERT: C 835 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8613 (mmm) REVERT: C 844 LYS cc_start: 0.8937 (tttm) cc_final: 0.8347 (mmpt) REVERT: C 858 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7858 (mmtt) REVERT: C 861 GLU cc_start: 0.8610 (tp30) cc_final: 0.7986 (tt0) REVERT: C 864 MET cc_start: 0.8137 (ttm) cc_final: 0.6933 (tpp) REVERT: C 942 MET cc_start: 0.8253 (ttm) cc_final: 0.7764 (tmt) REVERT: C 943 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7481 (mp) REVERT: C 997 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8327 (m) outliers start: 69 outliers final: 37 residues processed: 299 average time/residue: 0.6477 time to fit residues: 221.2948 Evaluate side-chains 299 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG 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 355 MET 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 630 LYS Chi-restraints excluded: chain A residue 744 SER 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 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 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 536 VAL 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 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 102 MET 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 229 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 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 619 VAL Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 858 LYS Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 909 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 298 optimal weight: 5.9990 chunk 235 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.0030 chunk 270 optimal weight: 0.4980 chunk 230 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 534 HIS C 120 GLN C 691 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092424 restraints weight = 38425.541| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.14 r_work: 0.3084 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24075 Z= 0.111 Angle : 0.574 13.130 32601 Z= 0.284 Chirality : 0.041 0.134 3879 Planarity : 0.004 0.041 4086 Dihedral : 5.726 53.908 3354 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.61 % Allowed : 20.19 % Favored : 77.21 % 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: 0.05 (0.16), residues: 3063 helix: 0.64 (0.13), residues: 1635 sheet: -0.22 (0.22), residues: 552 loop : -0.71 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 117 TYR 0.017 0.001 TYR B 883 PHE 0.030 0.001 PHE B 4 TRP 0.005 0.001 TRP C 556 HIS 0.007 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (24075) covalent geometry : angle 0.57412 / 0.28 (32601) hydrogen bonds : bond 0.03525 / 2.33 ( 1132) hydrogen bonds : angle 3.86552 / 2.66 ( 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 312 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6286 (mmm) cc_final: 0.5755 (mpp) REVERT: A 89 GLU cc_start: 0.8415 (tt0) cc_final: 0.8046 (tp30) REVERT: A 101 GLU cc_start: 0.8563 (tp30) cc_final: 0.8275 (tp30) REVERT: A 120 GLN cc_start: 0.8862 (mp10) cc_final: 0.8570 (mm110) REVERT: A 128 GLN cc_start: 0.7857 (mp10) cc_final: 0.7579 (mp10) REVERT: A 165 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8316 (pp20) REVERT: A 338 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 355 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7318 (mtp) REVERT: A 525 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: A 529 LEU cc_start: 0.8631 (tp) cc_final: 0.8280 (mm) REVERT: A 590 GLN cc_start: 0.8210 (tp40) cc_final: 0.7698 (tt0) REVERT: A 649 ASN cc_start: 0.8423 (m110) cc_final: 0.7620 (p0) REVERT: A 706 MET cc_start: 0.6934 (mtm) cc_final: 0.5626 (tpt) REVERT: A 783 MET cc_start: 0.9424 (tpt) cc_final: 0.9136 (tpp) REVERT: A 844 LYS cc_start: 0.8767 (tttm) cc_final: 0.8094 (mppt) REVERT: A 849 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 864 MET cc_start: 0.8084 (ttm) cc_final: 0.6895 (tpp) REVERT: A 938 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: A 961 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7673 (mtt180) REVERT: B 1 MET cc_start: 0.5956 (mmm) cc_final: 0.5549 (mmm) REVERT: B 67 ARG cc_start: 0.8701 (ptm-80) cc_final: 0.8125 (ptm-80) REVERT: B 68 GLU cc_start: 0.8181 (mp0) cc_final: 0.7600 (mp0) REVERT: B 128 GLN cc_start: 0.7842 (mp10) cc_final: 0.7508 (mp10) REVERT: B 134 SER cc_start: 0.8466 (m) cc_final: 0.8198 (p) REVERT: B 292 GLN cc_start: 0.8449 (mt0) cc_final: 0.8188 (mt0) REVERT: B 353 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 398 MET cc_start: 0.8335 (mmm) cc_final: 0.7838 (mmm) REVERT: B 529 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 553 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8077 (mmp) REVERT: B 633 THR cc_start: 0.7384 (p) cc_final: 0.7155 (t) REVERT: B 637 SER cc_start: 0.8502 (t) cc_final: 0.8128 (m) REVERT: B 706 MET cc_start: 0.6796 (ttt) cc_final: 0.6321 (mtp) REVERT: B 844 LYS cc_start: 0.8861 (tttm) cc_final: 0.8365 (mmpt) REVERT: B 888 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7065 (tt) REVERT: C 1 MET cc_start: 0.6249 (mmm) cc_final: 0.5912 (mmm) REVERT: C 102 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7306 (mmm) REVERT: C 128 GLN cc_start: 0.7843 (mt0) cc_final: 0.7604 (mp10) REVERT: C 164 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8049 (pt0) REVERT: C 165 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8455 (pp20) REVERT: C 256 ASN cc_start: 0.8057 (p0) cc_final: 0.7825 (p0) REVERT: C 292 GLN cc_start: 0.8629 (mt0) cc_final: 0.8350 (mt0) REVERT: C 425 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5688 (tp) REVERT: C 449 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8753 (tp) REVERT: C 512 TRP cc_start: 0.7594 (t60) cc_final: 0.7309 (t60) REVERT: C 538 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6717 (mtp) REVERT: C 539 MET cc_start: 0.7771 (tpt) cc_final: 0.7511 (mmt) REVERT: C 633 THR cc_start: 0.7402 (p) cc_final: 0.7157 (t) REVERT: C 637 SER cc_start: 0.8460 (t) cc_final: 0.8042 (m) REVERT: C 706 MET cc_start: 0.7332 (mtp) cc_final: 0.6079 (tpt) REVERT: C 783 MET cc_start: 0.9391 (tpt) cc_final: 0.9182 (tpp) REVERT: C 835 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8604 (mmm) REVERT: C 844 LYS cc_start: 0.8934 (tttm) cc_final: 0.8343 (mmpt) REVERT: C 858 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7839 (mmtt) REVERT: C 861 GLU cc_start: 0.8595 (tp30) cc_final: 0.7962 (tt0) REVERT: C 864 MET cc_start: 0.8105 (ttm) cc_final: 0.6898 (tpp) REVERT: C 942 MET cc_start: 0.8218 (ttm) cc_final: 0.7729 (tmt) REVERT: C 943 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7453 (mp) REVERT: C 997 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8290 (m) outliers start: 67 outliers final: 34 residues processed: 294 average time/residue: 0.6363 time to fit residues: 214.2333 Evaluate side-chains 295 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 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 355 MET 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 630 LYS Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 759 MET 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 194 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 231 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 529 LEU 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 C residue 38 VAL Chi-restraints excluded: chain C residue 102 MET 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 229 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 348 MET 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 536 VAL Chi-restraints excluded: chain C residue 538 MET Chi-restraints excluded: chain C residue 619 VAL 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 943 LEU 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: 0.8980 chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 144 optimal weight: 0.0050 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN B 534 HIS 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 = 0.3567 r_free = 0.3567 target = 0.116896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092308 restraints weight = 38379.763| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.10 r_work: 0.3075 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4258 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= 0.129 Angle : 0.583 13.050 32601 Z= 0.288 Chirality : 0.042 0.137 3879 Planarity : 0.004 0.040 4086 Dihedral : 5.689 53.793 3354 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.37 % Allowed : 20.50 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 3063 helix: 0.66 (0.13), residues: 1635 sheet: -0.16 (0.22), residues: 546 loop : -0.75 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.019 0.001 TYR B 883 PHE 0.031 0.001 PHE C 824 TRP 0.006 0.001 TRP C 886 HIS 0.007 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (24075) covalent geometry : angle 0.58339 / 0.29 (32601) hydrogen bonds : bond 0.03666 / 2.42 ( 1132) hydrogen bonds : angle 3.89764 / 2.69 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7490.15 seconds wall clock time: 128 minutes 16.16 seconds (7696.16 seconds total)