Starting phenix.real_space_refine on Tue Aug 26 04:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.map" model { file = "/net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l43_62804/08_2025/9l43_62804.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.069 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 121 5.16 5 C 11058 2.51 5 N 2915 2.21 5 O 3170 1.98 5 H 15995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33261 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 11843 Classifications: {'peptide': 827} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 800} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 11, 'ASP:plan': 14, 'HIS:plan': 5, 'GLU:plan': 9, 'PHE:plan': 12, 'GLN:plan1': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 300 Chain: "B" Number of atoms: 11860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 11860 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 28, 'TRANS': 824} Chain breaks: 6 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 540 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 14, 'GLU:plan': 10, 'TYR:plan': 4, 'GLN:plan1': 14, 'HIS:plan': 5, 'ASN:plan1': 7, 'PHE:plan': 7, 'ASP:plan': 12, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 327 Chain: "D" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 4754 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 18, 'TRANS': 347} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'PHE:plan': 3, 'ARG:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 5, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 4802 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 18, 'TRANS': 350} Chain breaks: 6 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'GLU:plan': 4, 'HIS:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 146 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26553 SG CYS D 624 94.572 55.167 63.585 1.00 96.81 S ATOM 26620 SG CYS D 630 93.161 54.159 65.004 1.00 95.49 S ATOM 27198 SG CYS D 680 95.128 53.016 63.718 1.00112.06 S ATOM 27224 SG CYS D 682 93.318 51.943 64.526 1.00107.42 S ATOM 31350 SG CYS C 624 25.701 121.150 61.595 1.00 50.00 S ATOM 31374 SG CYS C 630 27.507 121.772 62.967 1.00 90.83 S ATOM 31968 SG CYS C 680 25.601 123.311 63.171 1.00105.62 S ATOM 31985 SG CYS C 682 27.792 123.933 63.017 1.00 94.89 S Time building chain proxies: 6.27, per 1000 atoms: 0.19 Number of scatterers: 33261 At special positions: 0 Unit cell: (120.91, 178.69, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 121 16.00 O 3170 8.00 N 2915 7.00 C 11058 6.00 H 15995 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 128 " distance=2.05 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 330 " - pdb=" SG CYS C 330 " distance=2.07 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 680 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 630 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 624 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 682 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 630 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 680 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 624 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 682 " Number of angles added : 12 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4646 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 2 sheets defined 78.8% alpha, 0.2% 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 10 through 19 Processing helix chain 'A' and resid 27 through 46 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.732A pdb=" N GLU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.640A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 137 removed outlier: 4.688A pdb=" N LYS A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 165 removed outlier: 3.971A pdb=" N PHE A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 4.040A pdb=" N HIS A 185 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 6.191A pdb=" N ALA A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 262 through 280 removed outlier: 3.669A pdb=" N ALA A 266 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N THR A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 303 removed outlier: 4.480A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.755A pdb=" N LEU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.958A pdb=" N ARG A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 412 removed outlier: 4.187A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 481 Processing helix chain 'A' and resid 488 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.646A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 4.165A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.820A pdb=" N LEU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.056A pdb=" N LYS A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 629 through 643 removed outlier: 3.517A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 664 through 683 removed outlier: 5.137A pdb=" N ILE A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.843A pdb=" N GLY A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.861A pdb=" N HIS A 792 " --> pdb=" O HIS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 815 removed outlier: 4.219A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N MET A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.650A pdb=" N VAL A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 840 through 861 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.761A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 949 removed outlier: 5.810A pdb=" N LYS A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Proline residue: A 932 - end of helix Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 25 through 45 removed outlier: 3.795A pdb=" N LYS B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix removed outlier: 3.596A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.789A pdb=" N VAL B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'B' and resid 65 through 79 removed outlier: 3.562A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 116 through 138 removed outlier: 3.906A pdb=" N LYS B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE B 132 " --> pdb=" O CYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 165 Processing helix chain 'B' and resid 198 through 221 removed outlier: 6.242A pdb=" N ALA B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.925A pdb=" N LEU B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 260 Processing helix chain 'B' and resid 262 through 281 removed outlier: 3.734A pdb=" N ALA B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 303 removed outlier: 5.230A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.632A pdb=" N LEU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.854A pdb=" N ARG B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 392 through 411 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 460 through 480 removed outlier: 3.793A pdb=" N SER B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 Processing helix chain 'B' and resid 536 through 553 removed outlier: 4.195A pdb=" N ARG B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 580 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.879A pdb=" N GLY B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 601 removed outlier: 4.509A pdb=" N TYR B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 601 " --> pdb=" O PRO B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 601' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.514A pdb=" N LYS B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.925A pdb=" N ASN B 616 " --> pdb=" O THR B 612 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 629 through 643 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.552A pdb=" N GLN B 661 " --> pdb=" O ASN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 683 removed outlier: 5.589A pdb=" N ILE B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 Processing helix chain 'B' and resid 700 through 718 removed outlier: 3.916A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.667A pdb=" N LYS B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 791 " --> pdb=" O HIS B 787 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS B 792 " --> pdb=" O HIS B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 811 Processing helix chain 'B' and resid 818 through 835 removed outlier: 4.343A pdb=" N LYS B 829 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 861 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 883 through 896 removed outlier: 3.525A pdb=" N PHE B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.767A pdb=" N THR B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 942 removed outlier: 5.234A pdb=" N LYS B 931 " --> pdb=" O SER B 927 " (cutoff:3.500A) Proline residue: B 932 - end of helix removed outlier: 3.840A pdb=" N GLU B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 318 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 419 through 434 Processing helix chain 'D' and resid 468 through 489 removed outlier: 3.979A pdb=" N GLY D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.820A pdb=" N LYS D 540 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 545 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 548 " --> pdb=" O HIS D 544 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 552 " --> pdb=" O PHE D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 557 Processing helix chain 'D' and resid 558 through 575 removed outlier: 4.197A pdb=" N THR D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 588 removed outlier: 3.783A pdb=" N CYS D 585 " --> pdb=" O ARG D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 Processing helix chain 'D' and resid 599 through 615 Processing helix chain 'D' and resid 616 through 623 removed outlier: 3.695A pdb=" N ALA D 620 " --> pdb=" O ASP D 617 " (cutoff:3.500A) Proline residue: D 621 - end of helix Processing helix chain 'D' and resid 633 through 641 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.181A pdb=" N SER D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 705 removed outlier: 4.322A pdb=" N VAL D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 702 " --> pdb=" O TRP D 698 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG D 703 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D 704 " --> pdb=" O THR D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 733 Processing helix chain 'D' and resid 736 through 742 Processing helix chain 'D' and resid 744 through 762 Proline residue: D 753 - end of helix Processing helix chain 'D' and resid 766 through 776 Processing helix chain 'C' and resid 310 through 317 removed outlier: 4.434A pdb=" N ASN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 371 through 390 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 419 through 440 removed outlier: 3.755A pdb=" N VAL C 423 " --> pdb=" O PHE C 419 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS C 430 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 489 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.536A pdb=" N ALA C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 548 " --> pdb=" O HIS C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 574 Processing helix chain 'C' and resid 579 through 588 removed outlier: 4.922A pdb=" N CYS C 585 " --> pdb=" O ARG C 582 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 588 " --> pdb=" O CYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.553A pdb=" N CYS C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 631 through 641 Processing helix chain 'C' and resid 648 through 668 Processing helix chain 'C' and resid 680 through 702 removed outlier: 4.589A pdb=" N VAL C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 710 through 734 Processing helix chain 'C' and resid 736 through 742 Processing helix chain 'C' and resid 744 through 762 Proline residue: C 753 - end of helix Processing helix chain 'C' and resid 766 through 777 removed outlier: 3.678A pdb=" N CYS C 777 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 454 through 455 removed outlier: 8.026A pdb=" N VAL A 454 " --> pdb=" O THR A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 removed outlier: 6.666A pdb=" N LYS B 452 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 1252 hydrogen bonds defined for protein. 3687 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: 7.66 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15941 1.05 - 1.26: 2957 1.26 - 1.47: 6601 1.47 - 1.68: 7863 1.68 - 1.89: 173 Bond restraints: 33535 Sorted by residual: bond pdb=" CA LEU C 623 " pdb=" C LEU C 623 " ideal model delta sigma weight residual 1.523 1.689 -0.166 1.34e-02 5.57e+03 1.53e+02 bond pdb=" C CYS C 624 " pdb=" N SER C 625 " ideal model delta sigma weight residual 1.333 1.248 0.085 1.45e-02 4.76e+03 3.42e+01 bond pdb=" CA CYS C 624 " pdb=" C CYS C 624 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.26e-02 6.30e+03 3.21e+01 bond pdb=" N LEU C 631 " pdb=" CA LEU C 631 " ideal model delta sigma weight residual 1.459 1.523 -0.064 1.21e-02 6.83e+03 2.76e+01 bond pdb=" ND1 HIS C 488 " pdb=" CE1 HIS C 488 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 ... (remaining 33530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.87: 60537 20.87 - 41.74: 10 41.74 - 62.61: 0 62.61 - 83.48: 1 83.48 - 104.35: 1 Bond angle restraints: 60549 Sorted by residual: angle pdb="HD22 LEU D 312 " pdb=" CD2 LEU D 312 " pdb="HD23 LEU D 312 " ideal model delta sigma weight residual 110.00 5.65 104.35 3.00e+00 1.11e-01 1.21e+03 angle pdb="HD22 LEU A 642 " pdb=" CD2 LEU A 642 " pdb="HD23 LEU A 642 " ideal model delta sigma weight residual 110.00 27.27 82.73 3.00e+00 1.11e-01 7.60e+02 angle pdb=" O GLN C 622 " pdb=" C GLN C 622 " pdb=" N LEU C 623 " ideal model delta sigma weight residual 122.59 90.11 32.48 1.33e+00 5.65e-01 5.96e+02 angle pdb=" N VAL A 822 " pdb=" CA VAL A 822 " pdb=" CB VAL A 822 " ideal model delta sigma weight residual 112.36 83.74 28.62 1.30e+00 5.92e-01 4.85e+02 angle pdb=" C CYS C 624 " pdb=" CA CYS C 624 " pdb=" CB CYS C 624 " ideal model delta sigma weight residual 110.77 86.61 24.16 1.67e+00 3.59e-01 2.09e+02 ... (remaining 60544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14248 17.62 - 35.25: 1252 35.25 - 52.87: 402 52.87 - 70.49: 122 70.49 - 88.12: 16 Dihedral angle restraints: 16040 sinusoidal: 8062 harmonic: 7978 Sorted by residual: dihedral pdb=" C HIS C 626 " pdb=" N HIS C 626 " pdb=" CA HIS C 626 " pdb=" CB HIS C 626 " ideal model delta harmonic sigma weight residual -122.60 -151.42 28.82 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N VAL A 822 " pdb=" C VAL A 822 " pdb=" CA VAL A 822 " pdb=" CB VAL A 822 " ideal model delta harmonic sigma weight residual 123.40 96.38 27.02 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" CA GLN C 622 " pdb=" C GLN C 622 " pdb=" N LEU C 623 " pdb=" CA LEU C 623 " ideal model delta harmonic sigma weight residual 180.00 126.75 53.25 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 16037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 2956 0.215 - 0.429: 5 0.429 - 0.644: 2 0.644 - 0.858: 0 0.858 - 1.073: 1 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA HIS C 626 " pdb=" N HIS C 626 " pdb=" C HIS C 626 " pdb=" CB HIS C 626 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA PHE D 383 " pdb=" N PHE D 383 " pdb=" C PHE D 383 " pdb=" CB PHE D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ARG A 821 " pdb=" N ARG A 821 " pdb=" C ARG A 821 " pdb=" CB ARG A 821 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 2961 not shown) Planarity restraints: 5327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 683 " -0.254 2.00e-02 2.50e+03 3.30e-01 1.64e+03 pdb=" CG ASN C 683 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN C 683 " 0.248 2.00e-02 2.50e+03 pdb=" ND2 ASN C 683 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 683 " -0.521 2.00e-02 2.50e+03 pdb="HD22 ASN C 683 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 35 " 0.229 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CD GLN A 35 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 35 " -0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN A 35 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN A 35 " -0.427 2.00e-02 2.50e+03 pdb="HE22 GLN A 35 " 0.438 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 622 " -0.112 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C GLN C 622 " 0.310 2.00e-02 2.50e+03 pdb=" O GLN C 622 " -0.105 2.00e-02 2.50e+03 pdb=" N LEU C 623 " -0.093 2.00e-02 2.50e+03 ... (remaining 5324 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 658 2.07 - 2.70: 53539 2.70 - 3.34: 98307 3.34 - 3.97: 112294 3.97 - 4.60: 177040 Nonbonded interactions: 441838 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 818 " pdb=" OE2 GLU A 864 " model vdw 1.439 2.450 nonbonded pdb=" O THR B 504 " pdb=" HG SER B 508 " model vdw 1.457 2.450 nonbonded pdb=" O TRP A 598 " pdb=" HG SER A 601 " model vdw 1.486 2.450 nonbonded pdb=" O VAL A 688 " pdb=" HZ2 LYS A 690 " model vdw 1.489 2.450 nonbonded pdb=" O LEU B 740 " pdb=" H ARG B 743 " model vdw 1.496 2.450 ... (remaining 441833 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 10 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 11 through \ 12 or (resid 13 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 14 through 15 or (resid 16 through 17 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 18 through 28 or (resi \ d 29 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 30 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 40 through 42 or (resid 43 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 44 through 55 or (resid 64 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 65 through 66 or (resid 67 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 68 or (resid 69 throug \ h 70 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 71 or (resid 72 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 73 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 78 through \ 85 or (resid 93 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 94 through 97 or (resid 98 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 99 through 116 or (resid 117 thro \ ugh 118 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 119 through 123 or (resid 124 through 129 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 130 or (resid 13 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 132 through 135 or (resid 136 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 137 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 146 through 147 or (resid 148 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 149 through 183 or (resid 192 and (name \ N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 o \ r name HB3)) or resid 193 through 195 or (resid 196 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 199 or (resid 200 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 201 through 216 or (resid 217 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 218 through 22 \ 1 or (resid 222 through 224 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 225 through 230 or (resid 231 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 232 thro \ ugh 234 or (resid 235 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 236 through 237 or (resid 238 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 239 through 24 \ 3 or (resid 244 through 246 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 247 through 257 or (resid 258 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 259 thro \ ugh 263 or (resid 264 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 265 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 287 through 298 or (resid 299 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 300 through 314 or (resid 315 an \ d (name N or name CA or name C or name O or name CB or name HA )) or (resid 316 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 317 through 324 or (resid 325 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 326 through 327 or (resid 328 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 329 through 335 or (resid 336 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 337 through 339 or (resid 340 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 341 t \ hrough 366 or (resid 367 through 369 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 370 through 376 or (resid 377 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 380 through 395 or (resid 396 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 397 through 399 o \ r (resid 400 through 401 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 402 through 407 or (resid 408 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 409 through \ 411 or (resid 412 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 413 through 457 or (resid 458 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 459 through 460 o \ r (resid 461 through 464 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 465 through 476 or (resid 477 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 478 through \ 483 or (resid 484 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 485 through 489 or (resid 490 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 491 through 501 o \ r (resid 502 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 503 through 509 or (resid 529 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or (resid 530 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 531 through 540 or (resid 541 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 542 through 549 or \ (resid 550 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 551 through 554 or (resid 555 through 556 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 557 through \ 602 or (resid 603 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 604 through 606 or (resid 607 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 608 or (resid 609 \ through 611 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 612 through 630 or (resid 631 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 632 through 640 or (resi \ d 641 through 643 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 644 or (resid 645 through 646 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 647 through 657 or \ (resid 658 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 659 through 662 or (resid 663 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name C or name O or name CB \ or name HA )) or resid 602 through 603 or (resid 604 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 605 through 611 or ( \ resid 612 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 613 through 617 or (resid 618 through 619 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 620 through 62 \ 5 or (resid 626 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 630 through 644 or (resid 645 through 646 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 647 thro \ ugh 650 or (resid 651 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 652 through 662 or (resid 663 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 664 or (resid \ 665 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 666 through 667 or (resid 668 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 669 or resid 680 or (resid 681 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 682 through 683 or (resid 684 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 685 through 693 or (resid 694 through \ 695 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 696 or (resid 697 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 698 through 699 or (resid 700 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 701 th \ rough 706 or (resid 707 through 708 and (name N or name CA or name C or name O o \ r name CB or name HA )) or resid 709 through 713 or (resid 714 through 716 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 717 through 729 or (resid 730 through 733 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 734 through 740 or (resid 741 \ through 742 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 743 through 754 or (resid 755 through 756 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 757 through \ 758 or (resid 759 through 760 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 761 through 768 or (resid 769 through 770 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 771 through 773 or (resid 774 through 775 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 776 through 801)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.250 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.840 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.016 0.935 17553 Z= 0.602 Angle : 1.120 53.873 23909 Z= 0.584 Chirality : 0.044 1.073 2964 Planarity : 0.007 0.179 3029 Dihedral : 14.188 88.118 5914 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.25 % Favored : 91.45 % Rotamer: Outliers : 0.37 % Allowed : 4.02 % Favored : 95.62 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.99 (0.13), residues: 2363 helix: -2.88 (0.09), residues: 1667 sheet: -4.45 (0.57), residues: 8 loop : -3.93 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 702 TYR 0.010 0.001 TYR B 397 PHE 0.021 0.002 PHE D 383 TRP 0.019 0.002 TRP B 598 HIS 0.008 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00572 (17540) covalent geometry : angle 0.91219 (23887) SS BOND : bond 0.01911 ( 5) SS BOND : angle 4.06142 ( 10) hydrogen bonds : bond 0.14787 ( 1252) hydrogen bonds : angle 7.23206 ( 3687) metal coordination : bond 0.68952 ( 8) metal coordination : angle 28.78616 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7193 (mmt) cc_final: 0.6732 (mmt) REVERT: D 377 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 636 TYR cc_start: 0.8313 (m-10) cc_final: 0.8071 (m-10) REVERT: C 685 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7880 (tm-30) REVERT: C 752 MET cc_start: 0.8274 (tpt) cc_final: 0.7985 (tpp) outliers start: 6 outliers final: 2 residues processed: 235 average time/residue: 0.2902 time to fit residues: 104.2356 Evaluate side-chains 169 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 630 CYS Chi-restraints excluded: chain C residue 680 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.102845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081187 restraints weight = 156728.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084298 restraints weight = 73551.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086208 restraints weight = 46558.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087203 restraints weight = 35198.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088006 restraints weight = 30125.811| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17553 Z= 0.172 Angle : 0.814 49.770 23909 Z= 0.355 Chirality : 0.038 0.453 2964 Planarity : 0.005 0.065 3029 Dihedral : 5.399 47.937 2481 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 1.22 % Allowed : 8.34 % Favored : 90.44 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.16), residues: 2363 helix: -0.91 (0.11), residues: 1724 sheet: -4.29 (0.63), residues: 8 loop : -2.86 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 645 TYR 0.013 0.001 TYR B 908 PHE 0.018 0.001 PHE D 383 TRP 0.013 0.001 TRP B 598 HIS 0.008 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00354 (17540) covalent geometry : angle 0.62781 (23887) SS BOND : bond 0.00780 ( 5) SS BOND : angle 4.14381 ( 10) hydrogen bonds : bond 0.05251 ( 1252) hydrogen bonds : angle 5.59933 ( 3687) metal coordination : bond 0.03384 ( 8) metal coordination : angle 22.82526 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 680 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6617 (t) REVERT: C 749 ASP cc_start: 0.8575 (m-30) cc_final: 0.8172 (m-30) REVERT: C 767 ASP cc_start: 0.7355 (t70) cc_final: 0.7120 (t70) outliers start: 20 outliers final: 11 residues processed: 210 average time/residue: 0.2933 time to fit residues: 96.6002 Evaluate side-chains 181 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 680 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN B 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079275 restraints weight = 155347.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082286 restraints weight = 74522.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084124 restraints weight = 47966.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085271 restraints weight = 36720.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085905 restraints weight = 31168.880| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17553 Z= 0.189 Angle : 0.769 45.086 23909 Z= 0.340 Chirality : 0.037 0.462 2964 Planarity : 0.005 0.069 3029 Dihedral : 5.015 55.356 2480 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 1.28 % Allowed : 10.23 % Favored : 88.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2363 helix: 0.12 (0.12), residues: 1733 sheet: -4.36 (0.72), residues: 8 loop : -2.50 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 223 TYR 0.011 0.001 TYR C 636 PHE 0.016 0.001 PHE D 383 TRP 0.031 0.002 TRP A 598 HIS 0.006 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00395 (17540) covalent geometry : angle 0.60083 (23887) SS BOND : bond 0.00823 ( 5) SS BOND : angle 4.20228 ( 10) hydrogen bonds : bond 0.04915 ( 1252) hydrogen bonds : angle 5.32459 ( 3687) metal coordination : bond 0.01612 ( 8) metal coordination : angle 21.07898 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7098 (mmt) cc_final: 0.6652 (mmt) REVERT: B 577 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8513 (pp30) REVERT: D 377 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7065 (tm-30) REVERT: D 767 ASP cc_start: 0.7412 (t70) cc_final: 0.7074 (t70) REVERT: C 749 ASP cc_start: 0.8614 (m-30) cc_final: 0.8296 (m-30) outliers start: 21 outliers final: 11 residues processed: 198 average time/residue: 0.2593 time to fit residues: 82.3547 Evaluate side-chains 179 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 471 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 30 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.101675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080506 restraints weight = 154715.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083341 restraints weight = 73196.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085081 restraints weight = 46821.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086184 restraints weight = 35821.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.086834 restraints weight = 30262.604| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17553 Z= 0.177 Angle : 0.742 43.736 23909 Z= 0.327 Chirality : 0.037 0.457 2964 Planarity : 0.005 0.070 3029 Dihedral : 4.768 37.556 2479 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 1.03 % Allowed : 11.99 % Favored : 86.98 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.17), residues: 2363 helix: 0.56 (0.12), residues: 1731 sheet: -4.20 (0.71), residues: 8 loop : -2.33 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 223 TYR 0.012 0.001 TYR C 636 PHE 0.016 0.001 PHE A 925 TRP 0.011 0.001 TRP D 652 HIS 0.004 0.001 HIS A 894 Details of bonding type rmsd covalent geometry : bond 0.00368 (17540) covalent geometry : angle 0.57846 (23887) SS BOND : bond 0.00887 ( 5) SS BOND : angle 3.70693 ( 10) hydrogen bonds : bond 0.04613 ( 1252) hydrogen bonds : angle 5.11975 ( 3687) metal coordination : bond 0.01499 ( 8) metal coordination : angle 20.50094 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7133 (tm-30) REVERT: D 767 ASP cc_start: 0.7416 (t70) cc_final: 0.7077 (t70) REVERT: C 548 PHE cc_start: 0.7696 (m-10) cc_final: 0.7430 (m-80) REVERT: C 749 ASP cc_start: 0.8569 (m-30) cc_final: 0.8268 (m-30) outliers start: 17 outliers final: 13 residues processed: 187 average time/residue: 0.2629 time to fit residues: 78.6773 Evaluate side-chains 180 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 16 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078986 restraints weight = 153639.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081983 restraints weight = 70315.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.083732 restraints weight = 44010.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.084862 restraints weight = 33612.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085445 restraints weight = 28319.595| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17553 Z= 0.142 Angle : 0.711 43.299 23909 Z= 0.307 Chirality : 0.036 0.458 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.583 36.820 2479 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 1.40 % Allowed : 12.84 % Favored : 85.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.18), residues: 2363 helix: 0.98 (0.13), residues: 1733 sheet: -4.12 (0.67), residues: 8 loop : -2.17 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 223 TYR 0.012 0.001 TYR C 636 PHE 0.016 0.001 PHE A 925 TRP 0.010 0.001 TRP D 652 HIS 0.003 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00300 (17540) covalent geometry : angle 0.54499 (23887) SS BOND : bond 0.00940 ( 5) SS BOND : angle 3.85478 ( 10) hydrogen bonds : bond 0.04307 ( 1252) hydrogen bonds : angle 4.86479 ( 3687) metal coordination : bond 0.01011 ( 8) metal coordination : angle 20.10556 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 377 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7226 (tm-30) REVERT: D 379 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: C 548 PHE cc_start: 0.7836 (m-80) cc_final: 0.7552 (m-80) REVERT: C 749 ASP cc_start: 0.8619 (m-30) cc_final: 0.8348 (m-30) outliers start: 23 outliers final: 13 residues processed: 205 average time/residue: 0.2620 time to fit residues: 87.0549 Evaluate side-chains 195 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 103 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 134 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.098673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076874 restraints weight = 154351.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079707 restraints weight = 72818.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081390 restraints weight = 46504.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082446 restraints weight = 35785.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082979 restraints weight = 30472.622| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17553 Z= 0.223 Angle : 0.766 40.577 23909 Z= 0.344 Chirality : 0.037 0.466 2964 Planarity : 0.005 0.071 3029 Dihedral : 4.628 37.211 2479 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.93 % Rotamer: Outliers : 1.58 % Allowed : 13.27 % Favored : 85.15 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2363 helix: 0.92 (0.12), residues: 1738 sheet: -4.25 (0.78), residues: 8 loop : -2.22 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 878 TYR 0.017 0.001 TYR C 636 PHE 0.019 0.001 PHE A 925 TRP 0.033 0.002 TRP A 598 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00460 (17540) covalent geometry : angle 0.60281 (23887) SS BOND : bond 0.00983 ( 5) SS BOND : angle 4.21419 ( 10) hydrogen bonds : bond 0.04525 ( 1252) hydrogen bonds : angle 5.07971 ( 3687) metal coordination : bond 0.01663 ( 8) metal coordination : angle 20.73307 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7275 (mmt) cc_final: 0.6761 (mmt) REVERT: B 76 MET cc_start: 0.8264 (tmm) cc_final: 0.8040 (tmm) REVERT: B 283 MET cc_start: 0.7864 (ttp) cc_final: 0.7626 (ttp) REVERT: D 377 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 379 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: D 589 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8609 (t) REVERT: C 548 PHE cc_start: 0.7966 (m-80) cc_final: 0.7716 (m-80) REVERT: C 749 ASP cc_start: 0.8670 (m-30) cc_final: 0.8408 (m-30) REVERT: C 752 MET cc_start: 0.8677 (tpt) cc_final: 0.8081 (tpp) outliers start: 26 outliers final: 19 residues processed: 193 average time/residue: 0.2708 time to fit residues: 83.9658 Evaluate side-chains 193 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 622 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 73 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 238 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 175 optimal weight: 0.6980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.078804 restraints weight = 152627.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081756 restraints weight = 69898.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083546 restraints weight = 43863.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084657 restraints weight = 33201.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.085225 restraints weight = 28054.259| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17553 Z= 0.122 Angle : 0.707 41.207 23909 Z= 0.298 Chirality : 0.036 0.462 2964 Planarity : 0.004 0.071 3029 Dihedral : 4.421 36.466 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 1.28 % Allowed : 13.94 % Favored : 84.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2363 helix: 1.40 (0.13), residues: 1731 sheet: -4.14 (0.79), residues: 8 loop : -2.03 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 718 TYR 0.015 0.001 TYR C 636 PHE 0.017 0.001 PHE D 383 TRP 0.015 0.001 TRP A 598 HIS 0.004 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00258 (17540) covalent geometry : angle 0.53625 (23887) SS BOND : bond 0.01037 ( 5) SS BOND : angle 3.43471 ( 10) hydrogen bonds : bond 0.04082 ( 1252) hydrogen bonds : angle 4.64790 ( 3687) metal coordination : bond 0.01008 ( 8) metal coordination : angle 20.34298 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7251 (mmt) cc_final: 0.6736 (mmt) REVERT: B 283 MET cc_start: 0.7766 (ttp) cc_final: 0.7473 (ttp) REVERT: D 377 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7324 (tm-30) REVERT: D 379 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: D 589 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8628 (t) REVERT: C 548 PHE cc_start: 0.7928 (m-80) cc_final: 0.7664 (m-80) REVERT: C 749 ASP cc_start: 0.8647 (m-30) cc_final: 0.8356 (m-30) outliers start: 21 outliers final: 14 residues processed: 210 average time/residue: 0.2676 time to fit residues: 89.3839 Evaluate side-chains 198 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 471 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 51 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078025 restraints weight = 153956.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080921 restraints weight = 72332.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082637 restraints weight = 45952.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083675 restraints weight = 35184.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.084334 restraints weight = 29995.059| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17553 Z= 0.163 Angle : 0.720 40.137 23909 Z= 0.312 Chirality : 0.036 0.460 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.398 36.454 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 1.46 % Allowed : 14.00 % Favored : 84.54 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2363 helix: 1.44 (0.13), residues: 1735 sheet: -4.15 (0.84), residues: 8 loop : -2.02 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 878 TYR 0.014 0.001 TYR A 397 PHE 0.022 0.001 PHE B 925 TRP 0.013 0.001 TRP A 598 HIS 0.006 0.001 HIS D 740 Details of bonding type rmsd covalent geometry : bond 0.00347 (17540) covalent geometry : angle 0.55286 (23887) SS BOND : bond 0.01930 ( 5) SS BOND : angle 4.22702 ( 10) hydrogen bonds : bond 0.04134 ( 1252) hydrogen bonds : angle 4.72621 ( 3687) metal coordination : bond 0.00992 ( 8) metal coordination : angle 20.23903 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7253 (mmt) cc_final: 0.6741 (mmt) REVERT: B 76 MET cc_start: 0.8353 (tmm) cc_final: 0.8000 (tmm) REVERT: B 283 MET cc_start: 0.7832 (ttp) cc_final: 0.7545 (ttp) REVERT: D 377 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 379 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8394 (mt0) REVERT: D 589 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 548 PHE cc_start: 0.7942 (m-80) cc_final: 0.7680 (m-80) REVERT: C 749 ASP cc_start: 0.8631 (m-30) cc_final: 0.8362 (m-30) outliers start: 24 outliers final: 18 residues processed: 205 average time/residue: 0.2676 time to fit residues: 87.7246 Evaluate side-chains 203 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 908 TYR Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079385 restraints weight = 152830.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082243 restraints weight = 71207.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083982 restraints weight = 45150.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085038 restraints weight = 34330.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085506 restraints weight = 29142.527| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17553 Z= 0.126 Angle : 0.708 39.910 23909 Z= 0.299 Chirality : 0.036 0.461 2964 Planarity : 0.004 0.071 3029 Dihedral : 4.321 36.142 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.20 % Rotamer: Outliers : 1.58 % Allowed : 14.24 % Favored : 84.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.18), residues: 2363 helix: 1.65 (0.13), residues: 1736 sheet: -4.07 (0.90), residues: 8 loop : -1.93 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 718 TYR 0.013 0.001 TYR A 397 PHE 0.018 0.001 PHE B 707 TRP 0.013 0.001 TRP A 598 HIS 0.004 0.001 HIS D 740 Details of bonding type rmsd covalent geometry : bond 0.00268 (17540) covalent geometry : angle 0.54226 (23887) SS BOND : bond 0.01533 ( 5) SS BOND : angle 3.82881 ( 10) hydrogen bonds : bond 0.03933 ( 1252) hydrogen bonds : angle 4.55664 ( 3687) metal coordination : bond 0.00894 ( 8) metal coordination : angle 20.05190 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8273 (tmm) cc_final: 0.8056 (tmm) REVERT: A 283 MET cc_start: 0.7235 (mmt) cc_final: 0.6704 (mmt) REVERT: A 813 MET cc_start: 0.7491 (mmp) cc_final: 0.7254 (mmp) REVERT: B 76 MET cc_start: 0.8389 (tmm) cc_final: 0.8031 (tmm) REVERT: B 197 MET cc_start: 0.8194 (mmm) cc_final: 0.7865 (mmm) REVERT: D 327 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8345 (mp) REVERT: D 377 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7331 (tm-30) REVERT: D 379 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: D 589 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8735 (t) REVERT: C 548 PHE cc_start: 0.7934 (m-80) cc_final: 0.7646 (m-80) REVERT: C 749 ASP cc_start: 0.8671 (m-30) cc_final: 0.8369 (m-30) outliers start: 26 outliers final: 19 residues processed: 215 average time/residue: 0.2712 time to fit residues: 93.0377 Evaluate side-chains 209 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 573 GLU Chi-restraints excluded: chain C residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 103 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.079446 restraints weight = 155255.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082395 restraints weight = 72811.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084205 restraints weight = 46522.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085316 restraints weight = 35563.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085903 restraints weight = 30231.452| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.002 0.079 17553 Z= 0.109 Angle : 0.690 40.812 23909 Z= 0.286 Chirality : 0.035 0.461 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.165 35.844 2479 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 1.52 % Allowed : 14.30 % Favored : 84.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.18), residues: 2363 helix: 1.85 (0.13), residues: 1736 sheet: -3.98 (0.94), residues: 8 loop : -1.77 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 703 TYR 0.012 0.001 TYR A 397 PHE 0.020 0.001 PHE D 383 TRP 0.013 0.001 TRP A 598 HIS 0.005 0.001 HIS B 509 Details of bonding type rmsd covalent geometry : bond 0.00236 (17540) covalent geometry : angle 0.52235 (23887) SS BOND : bond 0.01271 ( 5) SS BOND : angle 3.45944 ( 10) hydrogen bonds : bond 0.03688 ( 1252) hydrogen bonds : angle 4.38379 ( 3687) metal coordination : bond 0.00760 ( 8) metal coordination : angle 19.89543 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 11 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 93 is missing expected H atoms. Skipping. Residue ILE 103 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue SER 246 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue SER 464 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue MET 489 is missing expected H atoms. Skipping. Residue VAL 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue THR 504 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue TYR 570 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LEU 594 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue SER 629 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue ILE 677 is missing expected H atoms. Skipping. Residue LEU 679 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LYS 704 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue LEU 806 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue LEU 809 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue VAL 920 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue THR 947 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue TYR 26 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue MET 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 77 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue SER 198 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue ILE 244 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 328 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue ILE 408 is missing expected H atoms. Skipping. Residue LYS 452 is missing expected H atoms. Skipping. Residue ILE 461 is missing expected H atoms. Skipping. Residue LEU 462 is missing expected H atoms. Skipping. Residue LEU 477 is missing expected H atoms. Skipping. Residue LYS 483 is missing expected H atoms. Skipping. Residue LEU 490 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Residue VAL 530 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue LEU 550 is missing expected H atoms. Skipping. Residue LYS 556 is missing expected H atoms. Skipping. Residue THR 562 is missing expected H atoms. Skipping. Residue VAL 567 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue THR 611 is missing expected H atoms. Skipping. Residue SER 634 is missing expected H atoms. Skipping. Residue THR 641 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue TYR 656 is missing expected H atoms. Skipping. Residue LEU 660 is missing expected H atoms. Skipping. Residue SER 662 is missing expected H atoms. Skipping. Residue SER 663 is missing expected H atoms. Skipping. Residue VAL 672 is missing expected H atoms. Skipping. Residue LEU 678 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue LYS 690 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue LEU 692 is missing expected H atoms. Skipping. Residue ILE 693 is missing expected H atoms. Skipping. Residue LYS 697 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue THR 717 is missing expected H atoms. Skipping. Residue MET 721 is missing expected H atoms. Skipping. Residue TYR 723 is missing expected H atoms. Skipping. Residue THR 729 is missing expected H atoms. Skipping. Residue SER 749 is missing expected H atoms. Skipping. Residue SER 754 is missing expected H atoms. Skipping. Residue SER 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue LEU 758 is missing expected H atoms. Skipping. Residue SER 761 is missing expected H atoms. Skipping. Residue LYS 771 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LYS 773 is missing expected H atoms. Skipping. Residue ILE 774 is missing expected H atoms. Skipping. Residue SER 776 is missing expected H atoms. Skipping. Residue VAL 778 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue LEU 793 is missing expected H atoms. Skipping. Residue THR 808 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue ILE 828 is missing expected H atoms. Skipping. Residue LYS 829 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue LYS 843 is missing expected H atoms. Skipping. Residue VAL 847 is missing expected H atoms. Skipping. Residue LEU 848 is missing expected H atoms. Skipping. Residue LYS 851 is missing expected H atoms. Skipping. Residue TYR 854 is missing expected H atoms. Skipping. Residue ILE 859 is missing expected H atoms. Skipping. Residue THR 872 is missing expected H atoms. Skipping. Residue ILE 876 is missing expected H atoms. Skipping. Residue LYS 881 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue LEU 893 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue VAL 903 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue SER 924 is missing expected H atoms. Skipping. Residue SER 927 is missing expected H atoms. Skipping. Residue LYS 931 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 325 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue SER 336 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue MET 541 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LYS 566 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 586 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue VAL 603 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LEU 633 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue VAL 646 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 716 is missing expected H atoms. Skipping. Residue LEU 720 is missing expected H atoms. Skipping. Residue LEU 736 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 742 is missing expected H atoms. Skipping. Residue LEU 745 is missing expected H atoms. Skipping. Residue MET 752 is missing expected H atoms. Skipping. Residue LEU 762 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LEU 372 is missing expected H atoms. Skipping. Residue LEU 375 is missing expected H atoms. Skipping. Residue LEU 410 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Residue VAL 417 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue LEU 437 is missing expected H atoms. Skipping. Residue SER 467 is missing expected H atoms. Skipping. Residue VAL 468 is missing expected H atoms. Skipping. Residue ILE 470 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue ILE 481 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue LEU 496 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue VAL 560 is missing expected H atoms. Skipping. Residue LEU 565 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue SER 576 is missing expected H atoms. Skipping. Residue LEU 590 is missing expected H atoms. Skipping. Residue SER 595 is missing expected H atoms. Skipping. Residue THR 598 is missing expected H atoms. Skipping. Residue LEU 600 is missing expected H atoms. Skipping. Residue LEU 604 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 619 is missing expected H atoms. Skipping. Residue LEU 623 is missing expected H atoms. Skipping. Residue SER 625 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue SER 641 is missing expected H atoms. Skipping. Residue LEU 663 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue VAL 668 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue VAL 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue THR 700 is missing expected H atoms. Skipping. Residue LEU 730 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue LYS 733 is missing expected H atoms. Skipping. Residue MET 738 is missing expected H atoms. Skipping. Residue VAL 755 is missing expected H atoms. Skipping. Residue SER 756 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ALA 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.7231 (mmt) cc_final: 0.6683 (mmt) REVERT: A 933 ILE cc_start: 0.8974 (mt) cc_final: 0.8692 (mt) REVERT: B 76 MET cc_start: 0.8389 (tmm) cc_final: 0.8017 (tmm) REVERT: B 197 MET cc_start: 0.8120 (mmm) cc_final: 0.7818 (mmm) REVERT: B 512 MET cc_start: 0.8049 (ptt) cc_final: 0.7801 (ptt) REVERT: D 377 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 379 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: D 589 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8718 (t) REVERT: C 548 PHE cc_start: 0.7916 (m-80) cc_final: 0.7598 (m-80) REVERT: C 749 ASP cc_start: 0.8675 (m-30) cc_final: 0.8360 (m-30) outliers start: 25 outliers final: 16 residues processed: 221 average time/residue: 0.2653 time to fit residues: 94.1478 Evaluate side-chains 209 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 199 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 225 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.078607 restraints weight = 154007.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081517 restraints weight = 71320.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083310 restraints weight = 45150.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.084386 restraints weight = 34240.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084995 restraints weight = 29040.397| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 17553 Z= 0.162 Angle : 0.741 41.167 23909 Z= 0.324 Chirality : 0.036 0.460 2964 Planarity : 0.004 0.070 3029 Dihedral : 4.158 35.628 2479 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.20 % Rotamer: Outliers : 1.16 % Allowed : 15.22 % Favored : 83.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2363 helix: 1.82 (0.13), residues: 1739 sheet: -4.01 (0.99), residues: 8 loop : -1.79 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 703 TYR 0.018 0.001 TYR A 397 PHE 0.018 0.001 PHE B 707 TRP 0.012 0.001 TRP A 598 HIS 0.004 0.001 HIS D 740 Details of bonding type rmsd covalent geometry : bond 0.00364 (17540) covalent geometry : angle 0.57736 (23887) SS BOND : bond 0.02569 ( 5) SS BOND : angle 6.42804 ( 10) hydrogen bonds : bond 0.03883 ( 1252) hydrogen bonds : angle 4.54846 ( 3687) metal coordination : bond 0.00823 ( 8) metal coordination : angle 19.90643 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5038.92 seconds wall clock time: 87 minutes 10.54 seconds (5230.54 seconds total)