Starting phenix.real_space_refine on Fri Oct 30 07:18:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.map" model { file = "/net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5m_55589/10_2026/9t5m_55589.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 22374 2.51 5 N 5706 2.21 5 O 6078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.13s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Chain: "C" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 672} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 672} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Chain: "B" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Chain: "D" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Chain: "F" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 672} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 672} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Chain: "E" Number of atoms: 5728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 702, 5723 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 5846 Time building chain proxies: 12.43, per 1000 atoms: 0.36 Number of scatterers: 34368 At special positions: 0 Unit cell: (138.012, 154.938, 183.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6078 8.00 N 5706 7.00 C 22374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 339 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 354 " distance=2.03 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 339 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 354 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 339 " 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: 2.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8232 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 24 sheets defined 53.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.506A pdb=" N LEU A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.918A pdb=" N HIS A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.717A pdb=" N PHE A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.874A pdb=" N LEU A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 186 through 206 removed outlier: 4.235A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.825A pdb=" N LYS A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 299 removed outlier: 3.866A pdb=" N GLU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 328 removed outlier: 4.242A pdb=" N ASN A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 389 removed outlier: 3.623A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.673A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 4.286A pdb=" N SER A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.540A pdb=" N GLN A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 529 through 539 removed outlier: 4.245A pdb=" N SER A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.686A pdb=" N TYR A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 559 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 removed outlier: 4.146A pdb=" N GLU A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.653A pdb=" N ILE A 606 " --> pdb=" O PRO A 603 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.553A pdb=" N ILE A 677 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 680 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.997A pdb=" N LEU A 728 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 removed outlier: 3.790A pdb=" N GLY A 749 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 791 through 797 removed outlier: 3.765A pdb=" N SER A 795 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 removed outlier: 3.868A pdb=" N LEU A 817 " --> pdb=" O PRO A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.683A pdb=" N THR A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.555A pdb=" N LEU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.572A pdb=" N LEU C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 142 through 157 removed outlier: 3.689A pdb=" N HIS C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 164 through 179 removed outlier: 3.810A pdb=" N LEU C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 186 through 206 removed outlier: 4.103A pdb=" N LYS C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.901A pdb=" N LYS C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 298 removed outlier: 3.866A pdb=" N GLU C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 326 Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.720A pdb=" N ILE C 333 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 390 removed outlier: 4.594A pdb=" N ILE C 390 " --> pdb=" O TRP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.566A pdb=" N VAL C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 426 " --> pdb=" O MET C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 435 removed outlier: 4.279A pdb=" N SER C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 439 through 455 Processing helix chain 'C' and resid 456 through 462 removed outlier: 3.647A pdb=" N ARG C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 489 removed outlier: 3.548A pdb=" N PHE C 487 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.830A pdb=" N ILE C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER C 510 " --> pdb=" O ALA C 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 506 through 510' Processing helix chain 'C' and resid 529 through 539 removed outlier: 4.303A pdb=" N SER C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 553 through 559 removed outlier: 3.637A pdb=" N LEU C 559 " --> pdb=" O VAL C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 removed outlier: 3.881A pdb=" N GLU C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 613 Proline residue: C 611 - end of helix Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.620A pdb=" N LYS C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 633 " --> pdb=" O ASN C 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 628 through 633' Processing helix chain 'C' and resid 653 through 657 Processing helix chain 'C' and resid 673 through 682 removed outlier: 3.749A pdb=" N ILE C 677 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 680 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 removed outlier: 3.894A pdb=" N THR C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 728 removed outlier: 3.511A pdb=" N SER C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 728 " --> pdb=" O VAL C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.891A pdb=" N CYS C 774 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 797 removed outlier: 3.636A pdb=" N SER C 795 " --> pdb=" O GLU C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 820 removed outlier: 3.512A pdb=" N LEU C 817 " --> pdb=" O PRO C 814 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 818 " --> pdb=" O ALA C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 838 removed outlier: 3.625A pdb=" N THR C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 848 removed outlier: 3.918A pdb=" N LEU C 846 " --> pdb=" O VAL C 842 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN C 847 " --> pdb=" O LYS C 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.557A pdb=" N LEU B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 142 through 155 removed outlier: 3.717A pdb=" N HIS B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 189 through 205 Processing helix chain 'B' and resid 206 through 215 removed outlier: 4.191A pdb=" N THR B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 300 removed outlier: 3.683A pdb=" N GLU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 328 removed outlier: 3.607A pdb=" N LYS B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN B 328 " --> pdb=" O CYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 390 removed outlier: 4.686A pdb=" N ILE B 390 " --> pdb=" O TRP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.566A pdb=" N PHE B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 426 " --> pdb=" O MET B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.319A pdb=" N SER B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 455 Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.512A pdb=" N HIS B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.588A pdb=" N PHE B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 489 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 553 through 559 removed outlier: 4.044A pdb=" N LEU B 559 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 Processing helix chain 'B' and resid 605 through 610 removed outlier: 4.197A pdb=" N VAL B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 613 No H-bonds generated for 'chain 'B' and resid 611 through 613' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 673 through 682 removed outlier: 3.668A pdb=" N ILE B 677 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 680 " --> pdb=" O ILE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 removed outlier: 3.510A pdb=" N THR B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 4.028A pdb=" N LEU B 728 " --> pdb=" O VAL B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 751 removed outlier: 3.728A pdb=" N GLY B 749 " --> pdb=" O ILE B 746 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 751 " --> pdb=" O ILE B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 774 removed outlier: 3.550A pdb=" N PHE B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 797 removed outlier: 3.922A pdb=" N SER B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 removed outlier: 4.121A pdb=" N LEU B 817 " --> pdb=" O PRO B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 837 removed outlier: 3.597A pdb=" N THR B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 848 removed outlier: 3.662A pdb=" N GLN B 848 " --> pdb=" O GLU B 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.528A pdb=" N LEU D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 142 through 155 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 181 through 186 removed outlier: 3.664A pdb=" N TYR D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 206 removed outlier: 4.664A pdb=" N SER D 191 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 4.381A pdb=" N THR D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 211 " --> pdb=" O PRO D 207 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 300 removed outlier: 4.532A pdb=" N GLU D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 326 removed outlier: 3.798A pdb=" N ILE D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 387 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 427 through 437 removed outlier: 4.352A pdb=" N SER D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 Processing helix chain 'D' and resid 456 through 464 removed outlier: 3.566A pdb=" N HIS D 463 " --> pdb=" O LYS D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.376A pdb=" N PHE D 487 " --> pdb=" O PRO D 483 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 483 through 488' Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 553 through 559 removed outlier: 3.578A pdb=" N VAL D 556 " --> pdb=" O PRO D 553 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 559 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 613 removed outlier: 3.676A pdb=" N ILE D 606 " --> pdb=" O PRO D 603 " (cutoff:3.500A) Proline residue: D 611 - end of helix Processing helix chain 'D' and resid 629 through 634 Processing helix chain 'D' and resid 651 through 656 removed outlier: 4.209A pdb=" N PHE D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 682 removed outlier: 3.647A pdb=" N ILE D 677 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 681 " --> pdb=" O SER D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.790A pdb=" N THR D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 727 Processing helix chain 'D' and resid 745 through 751 removed outlier: 3.774A pdb=" N GLY D 749 " --> pdb=" O ILE D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 774 Processing helix chain 'D' and resid 791 through 797 removed outlier: 3.713A pdb=" N ILE D 794 " --> pdb=" O PRO D 791 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 795 " --> pdb=" O GLU D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 820 removed outlier: 3.550A pdb=" N CYS D 820 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 837 removed outlier: 3.886A pdb=" N ASP D 836 " --> pdb=" O ASP D 832 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 847 removed outlier: 3.725A pdb=" N ASN D 847 " --> pdb=" O LYS D 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 142 through 157 removed outlier: 3.889A pdb=" N HIS F 155 " --> pdb=" O GLN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 179 removed outlier: 3.693A pdb=" N LYS F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE F 165 " --> pdb=" O TYR F 161 " (cutoff:3.500A) Proline residue: F 166 - end of helix removed outlier: 3.618A pdb=" N LEU F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 Processing helix chain 'F' and resid 186 through 204 removed outlier: 4.295A pdb=" N SER F 191 " --> pdb=" O PRO F 187 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 199 " --> pdb=" O HIS F 195 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS F 202 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 204 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.818A pdb=" N THR F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 300 removed outlier: 3.563A pdb=" N GLU F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 326 removed outlier: 3.596A pdb=" N LYS F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 390 removed outlier: 4.476A pdb=" N ILE F 390 " --> pdb=" O TRP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 405 Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.699A pdb=" N PHE F 418 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR F 426 " --> pdb=" O MET F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 433 removed outlier: 4.196A pdb=" N SER F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 removed outlier: 3.631A pdb=" N PHE F 437 " --> pdb=" O PHE F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 455 Processing helix chain 'F' and resid 457 through 463 removed outlier: 3.580A pdb=" N ARG F 461 " --> pdb=" O PHE F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 Processing helix chain 'F' and resid 506 through 510 removed outlier: 3.643A pdb=" N ILE F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER F 510 " --> pdb=" O ALA F 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 506 through 510' Processing helix chain 'F' and resid 530 through 538 Processing helix chain 'F' and resid 548 through 552 Processing helix chain 'F' and resid 553 through 559 Processing helix chain 'F' and resid 603 through 613 removed outlier: 3.509A pdb=" N ILE F 606 " --> pdb=" O PRO F 603 " (cutoff:3.500A) Proline residue: F 611 - end of helix Processing helix chain 'F' and resid 628 through 633 removed outlier: 3.593A pdb=" N LYS F 632 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 633 " --> pdb=" O ASN F 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 628 through 633' Processing helix chain 'F' and resid 653 through 657 Processing helix chain 'F' and resid 673 through 682 removed outlier: 3.744A pdb=" N ILE F 677 " --> pdb=" O GLU F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.713A pdb=" N THR F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 728 removed outlier: 3.534A pdb=" N SER F 727 " --> pdb=" O ALA F 724 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU F 728 " --> pdb=" O VAL F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 751 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.527A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 797 removed outlier: 3.658A pdb=" N SER F 795 " --> pdb=" O GLU F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 820 removed outlier: 3.565A pdb=" N LEU F 817 " --> pdb=" O PRO F 814 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F 818 " --> pdb=" O ALA F 815 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS F 820 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 838 Processing helix chain 'F' and resid 839 through 847 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.557A pdb=" N LEU E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 142 through 157 removed outlier: 3.637A pdb=" N HIS E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 180 removed outlier: 3.727A pdb=" N LYS E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 165 " --> pdb=" O TYR E 161 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 4.023A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 removed outlier: 3.857A pdb=" N TYR E 186 " --> pdb=" O PHE E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 206 removed outlier: 3.848A pdb=" N SER E 191 " --> pdb=" O PRO E 187 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.848A pdb=" N LYS E 211 " --> pdb=" O PRO E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 299 removed outlier: 4.327A pdb=" N GLU E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 328 removed outlier: 3.529A pdb=" N ILE E 320 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN E 328 " --> pdb=" O CYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 389 Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 413 through 427 removed outlier: 3.600A pdb=" N LEU E 419 " --> pdb=" O ASP E 415 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 426 " --> pdb=" O MET E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 437 removed outlier: 4.351A pdb=" N SER E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL E 436 " --> pdb=" O LYS E 432 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 455 Processing helix chain 'E' and resid 456 through 464 removed outlier: 3.528A pdb=" N HIS E 463 " --> pdb=" O LYS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 489 removed outlier: 3.650A pdb=" N VAL E 486 " --> pdb=" O PRO E 483 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE E 487 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 530 through 539 Processing helix chain 'E' and resid 548 through 552 Processing helix chain 'E' and resid 553 through 558 removed outlier: 3.536A pdb=" N VAL E 556 " --> pdb=" O PRO E 553 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR E 557 " --> pdb=" O ALA E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 613 removed outlier: 3.550A pdb=" N ILE E 606 " --> pdb=" O PRO E 603 " (cutoff:3.500A) Proline residue: E 611 - end of helix Processing helix chain 'E' and resid 628 through 634 Processing helix chain 'E' and resid 651 through 656 removed outlier: 4.210A pdb=" N PHE E 655 " --> pdb=" O PRO E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 682 removed outlier: 3.735A pdb=" N ILE E 677 " --> pdb=" O GLU E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 705 removed outlier: 3.872A pdb=" N THR E 703 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 727 Processing helix chain 'E' and resid 745 through 751 removed outlier: 3.719A pdb=" N GLY E 749 " --> pdb=" O ILE E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 774 Processing helix chain 'E' and resid 791 through 797 removed outlier: 3.544A pdb=" N ILE E 794 " --> pdb=" O PRO E 791 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER E 795 " --> pdb=" O GLU E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 820 removed outlier: 3.790A pdb=" N LEU E 817 " --> pdb=" O PRO E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 837 removed outlier: 3.730A pdb=" N ASP E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR E 837 " --> pdb=" O GLN E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 847 removed outlier: 3.663A pdb=" N ASN E 847 " --> pdb=" O LYS E 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA2, first strand: chain 'A' and resid 465 through 466 removed outlier: 6.574A pdb=" N GLN A 472 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LYS A 496 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 474 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU A 498 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 476 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 495 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS A 521 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 497 " --> pdb=" O CYS A 521 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 518 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LYS A 545 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 520 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 565 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LYS A 596 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 567 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 640 " --> pdb=" O ASP A 664 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 663 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A 803 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AA5, first strand: chain 'C' and resid 464 through 466 removed outlier: 6.773A pdb=" N LEU C 495 " --> pdb=" O HIS C 519 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N CYS C 521 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU C 497 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 518 " --> pdb=" O HIS C 543 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS C 545 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 520 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 593 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N HIS C 619 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 595 " --> pdb=" O HIS C 619 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 616 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLN C 643 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 618 " --> pdb=" O GLN C 643 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS C 666 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 642 " --> pdb=" O LYS C 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 503 through 505 removed outlier: 5.957A pdb=" N ALA C 503 " --> pdb=" O LYS C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 688 through 689 removed outlier: 6.918A pdb=" N LEU C 688 " --> pdb=" O TYR C 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 756 through 758 Processing sheet with id=AA9, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 466 removed outlier: 6.707A pdb=" N GLN B 472 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS B 496 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 474 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU B 498 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 476 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 495 " --> pdb=" O HIS B 519 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS B 521 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 497 " --> pdb=" O CYS B 521 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 565 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS B 596 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 567 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 640 " --> pdb=" O ASP B 664 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 663 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 688 " --> pdb=" O TYR B 712 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU B 757 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 780 " --> pdb=" O GLU B 804 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 803 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'D' and resid 465 through 466 removed outlier: 6.391A pdb=" N GLN D 472 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS D 496 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU D 474 " --> pdb=" O LYS D 496 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU D 498 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU D 476 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 518 " --> pdb=" O HIS D 543 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LYS D 545 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU D 520 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 565 " --> pdb=" O HIS D 594 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LYS D 596 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 567 " --> pdb=" O LYS D 596 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU D 593 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS D 619 " --> pdb=" O LEU D 593 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL D 595 " --> pdb=" O HIS D 619 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 641 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 618 " --> pdb=" O GLU D 641 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU D 640 " --> pdb=" O ASP D 664 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU D 663 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU D 688 " --> pdb=" O TYR D 712 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 504 through 505 Processing sheet with id=AB6, first strand: chain 'D' and resid 756 through 758 removed outlier: 6.763A pdb=" N LEU D 803 " --> pdb=" O VAL D 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 336 through 339 Processing sheet with id=AB8, first strand: chain 'F' and resid 464 through 466 removed outlier: 6.019A pdb=" N GLN F 472 " --> pdb=" O VAL F 494 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS F 496 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 474 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU F 498 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU F 476 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 495 " --> pdb=" O HIS F 519 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N CYS F 521 " --> pdb=" O LEU F 495 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 497 " --> pdb=" O CYS F 521 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 518 " --> pdb=" O HIS F 543 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LYS F 545 " --> pdb=" O LEU F 518 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU F 520 " --> pdb=" O LYS F 545 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU F 593 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N HIS F 619 " --> pdb=" O LEU F 593 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL F 595 " --> pdb=" O HIS F 619 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU F 641 " --> pdb=" O LEU F 616 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 664 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU F 688 " --> pdb=" O TYR F 712 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 503 through 505 removed outlier: 5.680A pdb=" N ALA F 503 " --> pdb=" O LYS F 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 734 through 735 Processing sheet with id=AC2, first strand: chain 'F' and resid 803 through 804 removed outlier: 6.907A pdb=" N LEU F 803 " --> pdb=" O VAL F 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 336 through 339 Processing sheet with id=AC4, first strand: chain 'E' and resid 465 through 466 removed outlier: 6.719A pdb=" N LEU E 495 " --> pdb=" O HIS E 519 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N CYS E 521 " --> pdb=" O LEU E 495 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU E 497 " --> pdb=" O CYS E 521 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU E 518 " --> pdb=" O HIS E 543 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS E 545 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 520 " --> pdb=" O LYS E 545 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU E 542 " --> pdb=" O TYR E 566 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE E 568 " --> pdb=" O LEU E 542 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 544 " --> pdb=" O ILE E 568 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU E 565 " --> pdb=" O HIS E 594 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS E 596 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU E 567 " --> pdb=" O LYS E 596 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU E 640 " --> pdb=" O ASP E 664 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 663 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU E 688 " --> pdb=" O TYR E 712 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 503 through 505 Processing sheet with id=AC6, first strand: chain 'E' and resid 756 through 758 removed outlier: 6.768A pdb=" N LEU E 803 " --> pdb=" O VAL E 829 " (cutoff:3.500A) 1442 hydrogen bonds defined for protein. 3543 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: 6.76 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10756 1.34 - 1.46: 6826 1.46 - 1.58: 17260 1.58 - 1.69: 0 1.69 - 1.81: 306 Bond restraints: 35148 Sorted by residual: bond pdb=" C GLN F 511 " pdb=" N MET F 512 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.40e-02 5.10e+03 6.04e+00 bond pdb=" C GLN C 511 " pdb=" N MET C 512 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" CA GLN F 511 " pdb=" C GLN F 511 " ideal model delta sigma weight residual 1.519 1.538 -0.020 1.19e-02 7.06e+03 2.71e+00 bond pdb=" CA PRO B 699 " pdb=" C PRO B 699 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.22e+00 bond pdb=" CA GLN C 511 " pdb=" C GLN C 511 " ideal model delta sigma weight residual 1.520 1.538 -0.017 1.25e-02 6.40e+03 1.95e+00 ... (remaining 35143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 47222 1.96 - 3.91: 329 3.91 - 5.87: 31 5.87 - 7.82: 9 7.82 - 9.78: 7 Bond angle restraints: 47598 Sorted by residual: angle pdb=" C GLN C 511 " pdb=" N MET C 512 " pdb=" CA AMET C 512 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 angle pdb=" C GLN F 511 " pdb=" N MET F 512 " pdb=" CA BMET F 512 " ideal model delta sigma weight residual 121.70 131.46 -9.76 1.80e+00 3.09e-01 2.94e+01 angle pdb=" C GLN F 511 " pdb=" N MET F 512 " pdb=" CA AMET F 512 " ideal model delta sigma weight residual 121.70 131.43 -9.73 1.80e+00 3.09e-01 2.92e+01 angle pdb=" C GLN C 511 " pdb=" N MET C 512 " pdb=" CA BMET C 512 " ideal model delta sigma weight residual 121.70 131.39 -9.69 1.80e+00 3.09e-01 2.90e+01 angle pdb=" CA GLN C 511 " pdb=" C GLN C 511 " pdb=" N MET C 512 " ideal model delta sigma weight residual 118.22 123.55 -5.33 1.03e+00 9.43e-01 2.68e+01 ... (remaining 47593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 19913 16.43 - 32.87: 1108 32.87 - 49.30: 307 49.30 - 65.74: 65 65.74 - 82.17: 3 Dihedral angle restraints: 21396 sinusoidal: 8820 harmonic: 12576 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 354 " pdb=" CB CYS F 354 " ideal model delta sinusoidal sigma weight residual -86.00 -118.91 32.91 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 354 " pdb=" CB CYS C 354 " ideal model delta sinusoidal sigma weight residual -86.00 -118.83 32.83 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 354 " pdb=" CB CYS D 354 " ideal model delta sinusoidal sigma weight residual -86.00 -117.23 31.23 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 21393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3453 0.031 - 0.062: 1523 0.062 - 0.093: 344 0.093 - 0.124: 184 0.124 - 0.154: 28 Chirality restraints: 5532 Sorted by residual: chirality pdb=" CA GLN C 511 " pdb=" N GLN C 511 " pdb=" C GLN C 511 " pdb=" CB GLN C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA GLN F 511 " pdb=" N GLN F 511 " pdb=" C GLN F 511 " pdb=" CB GLN F 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 552 " pdb=" N ILE A 552 " pdb=" C ILE A 552 " pdb=" CB ILE A 552 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 5529 not shown) Planarity restraints: 5892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 390 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO D 391 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 391 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 391 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 409 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO F 410 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 410 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 410 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 390 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO E 391 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.018 5.00e-02 4.00e+02 ... (remaining 5889 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 21685 3.04 - 3.51: 36793 3.51 - 3.97: 57346 3.97 - 4.44: 70225 4.44 - 4.90: 105042 Nonbonded interactions: 291091 Sorted by model distance: nonbonded pdb=" O LYS E 138 " pdb=" OG1 THR E 139 " model vdw 2.576 3.040 nonbonded pdb=" N ASN A 414 " pdb=" CG ASN A 414 " model vdw 2.582 2.680 nonbonded pdb=" O LYS A 138 " pdb=" OG1 THR A 139 " model vdw 2.582 3.040 nonbonded pdb=" O LYS C 138 " pdb=" OG1 THR C 139 " model vdw 2.587 3.040 nonbonded pdb=" O LYS B 138 " pdb=" OG1 THR B 139 " model vdw 2.589 3.040 ... (remaining 291086 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 511 or resid 513 through 848)) selection = (chain 'B' and (resid 15 through 511 or resid 513 through 848)) selection = (chain 'C' and (resid 15 through 511 or resid 513 through 848)) selection = (chain 'D' and (resid 15 through 511 or resid 513 through 848)) selection = (chain 'E' and (resid 15 through 511 or resid 513 through 848)) selection = (chain 'F' and (resid 15 through 511 or resid 513 through 848)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 37.050 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.002 0.036 35160 Z= 0.108 Angle : 0.456 9.780 47622 Z= 0.240 Chirality : 0.039 0.154 5532 Planarity : 0.003 0.041 5892 Dihedral : 11.316 82.170 13128 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.62 % Favored : 96.24 % Rotamer: Outliers : 4.07 % Allowed : 7.12 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 4182 helix: -0.61 (0.12), residues: 1826 sheet: -1.65 (0.22), residues: 625 loop : 0.12 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 821 TYR 0.012 0.001 TYR A 186 PHE 0.014 0.001 PHE A 184 TRP 0.011 0.001 TRP A 24 HIS 0.003 0.000 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (35148) covalent geometry : angle 0.45522 / 0.24 (47598) SS BOND : bond 0.00305 / 0.19 ( 12) SS BOND : angle 0.96099 / 0.63 ( 24) hydrogen bonds : bond 0.23593 / 15.74 ( 1442) hydrogen bonds : angle 7.44873 / 5.27 ( 3543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 413 time to evaluate : 1.181 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: A 27 PHE cc_start: 0.8269 (t80) cc_final: 0.7727 (m-10) REVERT: A 37 MET cc_start: 0.8627 (tmm) cc_final: 0.8398 (tmt) REVERT: A 51 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8662 (pm20) REVERT: A 152 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9205 (tpp) REVERT: A 177 MET cc_start: 0.9142 (mmm) cc_final: 0.8820 (mtp) REVERT: A 336 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.9045 (pt0) REVERT: A 361 MET cc_start: 0.9337 (tpp) cc_final: 0.9116 (tpp) REVERT: A 390 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 397 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: A 408 ASP cc_start: 0.8251 (t0) cc_final: 0.7853 (t70) REVERT: A 422 MET cc_start: 0.9422 (mmm) cc_final: 0.9170 (mmm) REVERT: A 448 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 463 HIS cc_start: 0.9022 (t70) cc_final: 0.8544 (t-90) REVERT: A 478 MET cc_start: 0.8722 (mmm) cc_final: 0.8480 (mmm) REVERT: A 784 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: C 37 MET cc_start: 0.9303 (mtm) cc_final: 0.8900 (ttp) REVERT: C 194 GLU cc_start: 0.8851 (pt0) cc_final: 0.8527 (pp20) REVERT: C 355 THR cc_start: 0.9495 (OUTLIER) cc_final: 0.9197 (t) REVERT: C 390 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8659 (pp) REVERT: C 413 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7740 (pmtt) REVERT: C 422 MET cc_start: 0.9280 (mmm) cc_final: 0.9023 (mmm) REVERT: C 477 PHE cc_start: 0.8820 (t80) cc_final: 0.8415 (t80) REVERT: C 484 ASP cc_start: 0.8979 (m-30) cc_final: 0.8654 (p0) REVERT: C 528 GLU cc_start: 0.8322 (mp0) cc_final: 0.7642 (mm-30) REVERT: C 590 LEU cc_start: 0.9186 (tp) cc_final: 0.8967 (tm) REVERT: C 705 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6480 (m) REVERT: C 712 TYR cc_start: 0.9269 (m-80) cc_final: 0.8969 (m-10) REVERT: B 29 ASP cc_start: 0.8517 (t70) cc_final: 0.8235 (m-30) REVERT: B 165 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.8081 (t80) REVERT: B 194 GLU cc_start: 0.9056 (tp30) cc_final: 0.8612 (tp30) REVERT: B 202 LYS cc_start: 0.9080 (mttm) cc_final: 0.8753 (mtmt) REVERT: B 205 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8587 (pp20) REVERT: B 319 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7937 (t80) REVERT: B 378 PHE cc_start: 0.9009 (m-80) cc_final: 0.8660 (m-10) REVERT: B 390 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8208 (pp) REVERT: B 448 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8425 (pp20) REVERT: B 454 GLU cc_start: 0.9270 (tt0) cc_final: 0.9055 (tm-30) REVERT: B 478 MET cc_start: 0.8897 (mmm) cc_final: 0.8506 (mmm) REVERT: B 498 GLU cc_start: 0.9173 (tt0) cc_final: 0.8918 (tp30) REVERT: B 508 LYS cc_start: 0.9336 (tttp) cc_final: 0.9070 (ttpp) REVERT: B 511 GLN cc_start: 0.9076 (tt0) cc_final: 0.8805 (mt0) REVERT: B 545 LYS cc_start: 0.9447 (tttt) cc_final: 0.9219 (ttmm) REVERT: B 578 MET cc_start: 0.5776 (mpp) cc_final: 0.4800 (mmt) REVERT: B 662 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7377 (mp0) REVERT: B 804 GLU cc_start: 0.8356 (tt0) cc_final: 0.7969 (tt0) REVERT: B 822 MET cc_start: 0.8268 (ptp) cc_final: 0.7705 (pmm) REVERT: D 17 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7476 (p90) REVERT: D 202 LYS cc_start: 0.9132 (mttm) cc_final: 0.8785 (mmpt) REVERT: D 283 GLN cc_start: 0.9470 (mm-40) cc_final: 0.8940 (mm-40) REVERT: D 319 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8101 (t80) REVERT: F 27 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: F 35 MET cc_start: 0.8527 (mtp) cc_final: 0.8138 (ttm) REVERT: F 165 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7941 (m-10) REVERT: F 183 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.5133 (t60) REVERT: F 184 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: F 397 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6993 (t80) REVERT: F 399 LYS cc_start: 0.8858 (tptm) cc_final: 0.8542 (ttpp) REVERT: F 409 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4381 (tp) REVERT: F 415 ASP cc_start: 0.6783 (t0) cc_final: 0.5947 (m-30) REVERT: F 484 ASP cc_start: 0.8451 (m-30) cc_final: 0.8167 (p0) REVERT: F 615 LYS cc_start: 0.8999 (tttt) cc_final: 0.8709 (mptt) REVERT: F 690 LEU cc_start: 0.7609 (mt) cc_final: 0.7278 (mm) REVERT: F 805 LEU cc_start: 0.9301 (mt) cc_final: 0.9086 (pp) REVERT: E 51 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8765 (pm20) REVERT: E 184 PHE cc_start: 0.8642 (p90) cc_final: 0.7859 (p90) REVERT: E 346 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9077 (mt) REVERT: E 397 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7575 (t80) REVERT: E 422 MET cc_start: 0.8705 (mmm) cc_final: 0.8397 (mmm) REVERT: E 454 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7914 (tm-30) outliers start: 158 outliers final: 59 residues processed: 552 average time/residue: 0.5700 time to fit residues: 389.4080 Evaluate side-chains 333 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 249 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 184 PHE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 454 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.0870 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 30.0000 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 629 ASN A 833 GLN C 145 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 ASN ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN B 155 HIS B 181 ASN B 357 ASN B 428 GLN B 462 GLN B 511 GLN B 612 HIS B 629 ASN B 636 ASN B 692 HIS D 511 GLN D 636 ASN D 752 GLN D 819 GLN F 51 GLN F 145 GLN F 155 HIS F 297 HIS ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 629 ASN F 707 ASN ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 GLN E 636 ASN E 819 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.132468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079652 restraints weight = 177641.315| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.10 r_work: 0.3025 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35160 Z= 0.199 Angle : 0.660 14.491 47622 Z= 0.333 Chirality : 0.044 0.245 5532 Planarity : 0.004 0.045 5892 Dihedral : 7.767 93.571 4642 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.35 % Rotamer: Outliers : 4.20 % Allowed : 12.95 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 4182 helix: -0.31 (0.12), residues: 1892 sheet: -1.64 (0.22), residues: 615 loop : -0.13 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 812 TYR 0.024 0.002 TYR F 738 PHE 0.032 0.002 PHE F 294 TRP 0.021 0.001 TRP C 183 HIS 0.008 0.001 HIS A 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (35148) covalent geometry : angle 0.65977 / 0.33 (47598) SS BOND : bond 0.00508 / 0.29 ( 12) SS BOND : angle 1.14126 / 0.81 ( 24) hydrogen bonds : bond 0.05547 / 3.67 ( 1442) hydrogen bonds : angle 5.10785 / 3.58 ( 3543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 273 time to evaluate : 1.453 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: A 27 PHE cc_start: 0.8309 (t80) cc_final: 0.7763 (m-10) REVERT: A 37 MET cc_start: 0.8731 (tmm) cc_final: 0.8462 (tmt) REVERT: A 51 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: A 177 MET cc_start: 0.9198 (mmm) cc_final: 0.8809 (mtp) REVERT: A 336 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9046 (pt0) REVERT: A 390 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (pp) REVERT: A 397 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: A 408 ASP cc_start: 0.8309 (t0) cc_final: 0.8062 (p0) REVERT: A 409 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7507 (mm) REVERT: A 422 MET cc_start: 0.9210 (mmm) cc_final: 0.8942 (mmm) REVERT: A 448 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 463 HIS cc_start: 0.9073 (t70) cc_final: 0.8501 (t-90) REVERT: A 477 PHE cc_start: 0.9062 (t80) cc_final: 0.8766 (t80) REVERT: A 478 MET cc_start: 0.8776 (mmm) cc_final: 0.8559 (mmm) REVERT: A 484 ASP cc_start: 0.8823 (m-30) cc_final: 0.8498 (p0) REVERT: A 784 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: A 822 MET cc_start: 0.8603 (ptp) cc_final: 0.8303 (pmm) REVERT: C 37 MET cc_start: 0.9325 (mtm) cc_final: 0.8896 (ttp) REVERT: C 355 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9266 (t) REVERT: C 390 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8523 (pp) REVERT: C 473 GLU cc_start: 0.8977 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 477 PHE cc_start: 0.8738 (t80) cc_final: 0.8149 (t80) REVERT: C 484 ASP cc_start: 0.8909 (m-30) cc_final: 0.8578 (p0) REVERT: C 509 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7675 (pp) REVERT: C 529 GLN cc_start: 0.7558 (pm20) cc_final: 0.7048 (pm20) REVERT: C 578 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6185 (mmp) REVERT: C 590 LEU cc_start: 0.9228 (tp) cc_final: 0.9015 (tm) REVERT: C 712 TYR cc_start: 0.9343 (m-80) cc_final: 0.9061 (m-10) REVERT: B 29 ASP cc_start: 0.8471 (t70) cc_final: 0.8267 (m-30) REVERT: B 40 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8720 (tp) REVERT: B 165 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 194 GLU cc_start: 0.9050 (tp30) cc_final: 0.8590 (tp30) REVERT: B 202 LYS cc_start: 0.9037 (mttm) cc_final: 0.8777 (mtpt) REVERT: B 205 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8697 (pp20) REVERT: B 319 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7954 (t80) REVERT: B 325 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5545 (t80) REVERT: B 378 PHE cc_start: 0.9089 (m-80) cc_final: 0.8613 (m-10) REVERT: B 390 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8257 (pp) REVERT: B 448 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8449 (pp20) REVERT: B 463 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8989 (m90) REVERT: B 473 GLU cc_start: 0.8970 (tt0) cc_final: 0.8205 (pp20) REVERT: B 478 MET cc_start: 0.8883 (mmm) cc_final: 0.8669 (mmm) REVERT: B 498 GLU cc_start: 0.9184 (tt0) cc_final: 0.8882 (tp30) REVERT: B 508 LYS cc_start: 0.9169 (tttp) cc_final: 0.8848 (tppt) REVERT: B 511 GLN cc_start: 0.9132 (tt0) cc_final: 0.8906 (tt0) REVERT: B 545 LYS cc_start: 0.9436 (tttt) cc_final: 0.9226 (ttmm) REVERT: B 578 MET cc_start: 0.5730 (mpp) cc_final: 0.4959 (mmt) REVERT: B 662 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7431 (mp0) REVERT: B 805 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9150 (mm) REVERT: B 822 MET cc_start: 0.8097 (ptp) cc_final: 0.7627 (pmm) REVERT: D 17 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7297 (p90) REVERT: D 202 LYS cc_start: 0.9189 (mttm) cc_final: 0.8916 (mmpt) REVERT: D 283 GLN cc_start: 0.9487 (mm-40) cc_final: 0.8992 (mm-40) REVERT: D 319 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8050 (t80) REVERT: D 361 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8664 (tpp) REVERT: D 397 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: D 635 MET cc_start: 0.7154 (mmm) cc_final: 0.5993 (pmm) REVERT: D 691 TRP cc_start: 0.8836 (p90) cc_final: 0.8409 (p90) REVERT: F 27 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: F 165 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: F 177 MET cc_start: 0.6697 (tmt) cc_final: 0.6487 (tmm) REVERT: F 183 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.5515 (t60) REVERT: F 399 LYS cc_start: 0.8818 (tptm) cc_final: 0.8546 (tmmt) REVERT: F 416 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6939 (t80) REVERT: F 477 PHE cc_start: 0.9046 (p90) cc_final: 0.8581 (p90) REVERT: F 478 MET cc_start: 0.9101 (mpm) cc_final: 0.8784 (ppp) REVERT: F 484 ASP cc_start: 0.8366 (m-30) cc_final: 0.8163 (p0) REVERT: F 524 PRO cc_start: 0.8519 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: F 615 LYS cc_start: 0.9032 (tttt) cc_final: 0.8741 (mptt) REVERT: F 805 LEU cc_start: 0.9361 (mt) cc_final: 0.9024 (pp) REVERT: F 813 LEU cc_start: 0.8794 (mm) cc_final: 0.8355 (mm) REVERT: F 822 MET cc_start: 0.8169 (pmm) cc_final: 0.7767 (pp-130) REVERT: E 51 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8892 (pm20) REVERT: E 184 PHE cc_start: 0.8627 (p90) cc_final: 0.7864 (p90) REVERT: E 325 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.6915 (t80) REVERT: E 346 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9096 (mt) REVERT: E 397 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7505 (t80) REVERT: E 454 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8198 (tm-30) outliers start: 163 outliers final: 84 residues processed: 402 average time/residue: 0.5345 time to fit residues: 268.9512 Evaluate side-chains 348 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 234 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 183 TRP Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 466 ARG Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [280, 266, 367, 179, 50, 317, 61, 308, 12, 140, 305] chunk 280 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 367 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 140 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN C 155 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN D 692 HIS F 51 GLN F 195 HIS ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 833 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.132701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077789 restraints weight = 156695.781| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.05 r_work: 0.3084 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35160 Z= 0.142 Angle : 0.624 11.676 47622 Z= 0.309 Chirality : 0.043 0.232 5532 Planarity : 0.004 0.047 5892 Dihedral : 7.371 74.166 4620 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.07 % Rotamer: Outliers : 4.43 % Allowed : 13.54 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 4182 helix: -0.07 (0.12), residues: 1892 sheet: -1.60 (0.23), residues: 614 loop : -0.21 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 466 TYR 0.031 0.001 TYR D 712 PHE 0.024 0.002 PHE F 184 TRP 0.043 0.002 TRP E 555 HIS 0.007 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (35148) covalent geometry : angle 0.62301 / 0.31 (47598) SS BOND : bond 0.00538 / 0.31 ( 12) SS BOND : angle 1.44918 / 0.96 ( 24) hydrogen bonds : bond 0.04532 / 2.99 ( 1442) hydrogen bonds : angle 4.66983 / 3.29 ( 3543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 250 time to evaluate : 1.053 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: A 27 PHE cc_start: 0.8256 (t80) cc_final: 0.7717 (m-10) REVERT: A 37 MET cc_start: 0.8731 (tmm) cc_final: 0.8454 (tmt) REVERT: A 51 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: A 53 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9227 (m) REVERT: A 165 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 177 MET cc_start: 0.9215 (mmm) cc_final: 0.8813 (mtp) REVERT: A 355 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9306 (t) REVERT: A 390 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 397 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: A 408 ASP cc_start: 0.8172 (t0) cc_final: 0.7849 (t70) REVERT: A 409 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 422 MET cc_start: 0.9238 (mmm) cc_final: 0.8922 (mmm) REVERT: A 448 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 463 HIS cc_start: 0.9016 (t70) cc_final: 0.8484 (t-90) REVERT: A 477 PHE cc_start: 0.8965 (t80) cc_final: 0.8711 (t80) REVERT: A 478 MET cc_start: 0.8733 (mmm) cc_final: 0.8523 (mmm) REVERT: A 484 ASP cc_start: 0.8831 (m-30) cc_final: 0.8544 (p0) REVERT: A 635 MET cc_start: 0.8451 (pmm) cc_final: 0.8128 (pmm) REVERT: A 784 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: A 822 MET cc_start: 0.8700 (ptp) cc_final: 0.8285 (pmm) REVERT: C 37 MET cc_start: 0.9301 (mtm) cc_final: 0.8880 (ttp) REVERT: C 194 GLU cc_start: 0.8493 (pp20) cc_final: 0.8259 (pp20) REVERT: C 355 THR cc_start: 0.9605 (OUTLIER) cc_final: 0.9272 (t) REVERT: C 390 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8586 (pp) REVERT: C 414 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7858 (p0) REVERT: C 459 LYS cc_start: 0.9665 (tptm) cc_final: 0.9398 (tptp) REVERT: C 477 PHE cc_start: 0.8520 (t80) cc_final: 0.8219 (t80) REVERT: C 484 ASP cc_start: 0.8857 (m-30) cc_final: 0.8598 (p0) REVERT: C 509 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7618 (pp) REVERT: C 517 GLU cc_start: 0.7564 (mp0) cc_final: 0.7359 (mp0) REVERT: C 578 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5810 (mmp) REVERT: C 634 MET cc_start: 0.6879 (mmt) cc_final: 0.6676 (mmt) REVERT: C 635 MET cc_start: 0.8753 (pmt) cc_final: 0.8511 (pmm) REVERT: C 712 TYR cc_start: 0.9288 (m-80) cc_final: 0.8847 (m-10) REVERT: B 40 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 165 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7729 (t80) REVERT: B 194 GLU cc_start: 0.9038 (tp30) cc_final: 0.8552 (tp30) REVERT: B 202 LYS cc_start: 0.9085 (mttm) cc_final: 0.8809 (mtpt) REVERT: B 205 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8564 (pp20) REVERT: B 319 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7900 (t80) REVERT: B 325 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.5476 (t80) REVERT: B 378 PHE cc_start: 0.9058 (m-80) cc_final: 0.8531 (m-10) REVERT: B 390 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8257 (pp) REVERT: B 478 MET cc_start: 0.8806 (mmm) cc_final: 0.8597 (mmm) REVERT: B 498 GLU cc_start: 0.9104 (tt0) cc_final: 0.8831 (tp30) REVERT: B 508 LYS cc_start: 0.9206 (tttp) cc_final: 0.8783 (tppt) REVERT: B 511 GLN cc_start: 0.9118 (tt0) cc_final: 0.8814 (tt0) REVERT: B 578 MET cc_start: 0.5917 (mpp) cc_final: 0.5304 (mmt) REVERT: B 662 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7406 (mp0) REVERT: B 822 MET cc_start: 0.8010 (ptp) cc_final: 0.7548 (pmm) REVERT: D 17 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7142 (p90) REVERT: D 18 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8055 (mmm-85) REVERT: D 202 LYS cc_start: 0.9163 (mttm) cc_final: 0.8892 (mmpt) REVERT: D 319 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8048 (t80) REVERT: D 361 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8536 (tpp) REVERT: D 397 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: D 635 MET cc_start: 0.7152 (mmm) cc_final: 0.6070 (pmm) REVERT: D 822 MET cc_start: 0.3426 (tmm) cc_final: 0.2871 (mmm) REVERT: F 27 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: F 51 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: F 58 LEU cc_start: 0.9073 (mp) cc_final: 0.8671 (mp) REVERT: F 165 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: F 170 LEU cc_start: 0.8848 (mm) cc_final: 0.8476 (tp) REVERT: F 294 PHE cc_start: 0.5964 (t80) cc_final: 0.5603 (t80) REVERT: F 319 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7051 (t80) REVERT: F 399 LYS cc_start: 0.8854 (tptm) cc_final: 0.8632 (tmmt) REVERT: F 415 ASP cc_start: 0.6640 (t0) cc_final: 0.5894 (m-30) REVERT: F 416 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6490 (t80) REVERT: F 420 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8337 (tp) REVERT: F 477 PHE cc_start: 0.9035 (p90) cc_final: 0.8450 (p90) REVERT: F 524 PRO cc_start: 0.8483 (Cg_exo) cc_final: 0.8279 (Cg_endo) REVERT: F 615 LYS cc_start: 0.9045 (tttt) cc_final: 0.8748 (mptt) REVERT: F 782 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8533 (tm) REVERT: F 822 MET cc_start: 0.8137 (pmm) cc_final: 0.7663 (pp-130) REVERT: E 184 PHE cc_start: 0.8654 (p90) cc_final: 0.7861 (p90) REVERT: E 325 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.6955 (t80) REVERT: E 346 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9105 (mt) REVERT: E 397 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7608 (t80) REVERT: E 454 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (tm-30) outliers start: 172 outliers final: 82 residues processed: 387 average time/residue: 0.5606 time to fit residues: 271.9270 Evaluate side-chains 337 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 222 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 698 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 354 CYS Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [372, 120, 49, 256, 360, 62, 365, 100, 378, 39, 196] chunk 372 optimal weight: 0.7980 chunk 120 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 360 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 365 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 378 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 HIS ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 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 = 0.4369 r_free = 0.4369 target = 0.133288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078130 restraints weight = 150742.550| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.04 r_work: 0.3086 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35160 Z= 0.143 Angle : 0.621 10.810 47622 Z= 0.304 Chirality : 0.043 0.225 5532 Planarity : 0.004 0.042 5892 Dihedral : 7.114 59.771 4604 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 4.25 % Allowed : 14.02 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 4182 helix: 0.09 (0.12), residues: 1883 sheet: -1.56 (0.23), residues: 614 loop : -0.20 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 671 TYR 0.022 0.001 TYR F 738 PHE 0.026 0.001 PHE D 165 TRP 0.043 0.001 TRP E 555 HIS 0.006 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (35148) covalent geometry : angle 0.62076 / 0.30 (47598) SS BOND : bond 0.00552 / 0.31 ( 12) SS BOND : angle 1.19333 / 0.82 ( 24) hydrogen bonds : bond 0.04129 / 2.72 ( 1442) hydrogen bonds : angle 4.49889 / 3.17 ( 3543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 237 time to evaluate : 1.271 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: A 27 PHE cc_start: 0.8231 (t80) cc_final: 0.7705 (m-10) REVERT: A 37 MET cc_start: 0.8726 (tmm) cc_final: 0.8439 (tmt) REVERT: A 51 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: A 53 VAL cc_start: 0.9547 (OUTLIER) cc_final: 0.9196 (m) REVERT: A 165 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 177 MET cc_start: 0.9213 (mmm) cc_final: 0.8818 (mtp) REVERT: A 355 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9274 (t) REVERT: A 390 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8843 (pp) REVERT: A 397 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 408 ASP cc_start: 0.8115 (t0) cc_final: 0.7800 (t70) REVERT: A 409 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 422 MET cc_start: 0.9276 (mmm) cc_final: 0.8926 (mmm) REVERT: A 448 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 463 HIS cc_start: 0.9058 (t70) cc_final: 0.8510 (t-90) REVERT: A 477 PHE cc_start: 0.8960 (t80) cc_final: 0.8758 (t80) REVERT: A 478 MET cc_start: 0.8694 (mmm) cc_final: 0.8488 (mmm) REVERT: A 635 MET cc_start: 0.8497 (pmm) cc_final: 0.8242 (pmm) REVERT: A 784 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: A 822 MET cc_start: 0.8716 (ptp) cc_final: 0.8256 (pmm) REVERT: C 37 MET cc_start: 0.9273 (mtm) cc_final: 0.8878 (ttp) REVERT: C 355 THR cc_start: 0.9613 (OUTLIER) cc_final: 0.9283 (t) REVERT: C 390 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8589 (pp) REVERT: C 414 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7912 (p0) REVERT: C 459 LYS cc_start: 0.9667 (tptm) cc_final: 0.9421 (tptp) REVERT: C 477 PHE cc_start: 0.8360 (t80) cc_final: 0.8072 (t80) REVERT: C 509 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7711 (pp) REVERT: C 578 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5806 (mmp) REVERT: C 634 MET cc_start: 0.6817 (mmt) cc_final: 0.6433 (mmt) REVERT: C 635 MET cc_start: 0.8739 (pmt) cc_final: 0.8534 (pmm) REVERT: C 712 TYR cc_start: 0.9257 (m-80) cc_final: 0.8827 (m-10) REVERT: B 40 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 165 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 194 GLU cc_start: 0.9044 (tp30) cc_final: 0.8605 (tm-30) REVERT: B 202 LYS cc_start: 0.9051 (mttm) cc_final: 0.8751 (mtpt) REVERT: B 205 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8625 (pp20) REVERT: B 319 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 325 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.5538 (t80) REVERT: B 390 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8128 (pp) REVERT: B 478 MET cc_start: 0.8834 (mmm) cc_final: 0.8606 (mmm) REVERT: B 498 GLU cc_start: 0.9097 (tt0) cc_final: 0.8820 (tp30) REVERT: B 508 LYS cc_start: 0.9203 (tttp) cc_final: 0.8855 (tppt) REVERT: B 511 GLN cc_start: 0.9093 (tt0) cc_final: 0.8884 (tt0) REVERT: B 562 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8624 (tm) REVERT: B 578 MET cc_start: 0.5951 (mpp) cc_final: 0.5351 (mmt) REVERT: B 652 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6782 (t-90) REVERT: B 662 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7396 (mp0) REVERT: B 804 GLU cc_start: 0.8086 (tt0) cc_final: 0.7799 (pt0) REVERT: B 822 MET cc_start: 0.8022 (ptp) cc_final: 0.7524 (pmm) REVERT: D 17 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7120 (p90) REVERT: D 18 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8097 (mmm160) REVERT: D 202 LYS cc_start: 0.9175 (mttm) cc_final: 0.8932 (mmpt) REVERT: D 283 GLN cc_start: 0.9472 (mm-40) cc_final: 0.8912 (mm-40) REVERT: D 319 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7992 (t80) REVERT: D 361 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8596 (tpp) REVERT: D 397 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: D 555 TRP cc_start: 0.6668 (p-90) cc_final: 0.6066 (p90) REVERT: D 635 MET cc_start: 0.7130 (mmm) cc_final: 0.6273 (pmm) REVERT: F 27 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: F 28 MET cc_start: 0.7926 (tpp) cc_final: 0.7627 (mmm) REVERT: F 58 LEU cc_start: 0.9062 (mp) cc_final: 0.8678 (mp) REVERT: F 165 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: F 192 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6229 (mttp) REVERT: F 294 PHE cc_start: 0.5935 (t80) cc_final: 0.5501 (t80) REVERT: F 319 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7025 (t80) REVERT: F 420 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8353 (tp) REVERT: F 524 PRO cc_start: 0.8538 (Cg_exo) cc_final: 0.8335 (Cg_endo) REVERT: F 615 LYS cc_start: 0.9057 (tttt) cc_final: 0.8770 (mptt) REVERT: F 782 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8573 (tm) REVERT: F 790 LEU cc_start: 0.8828 (pt) cc_final: 0.8358 (tm) REVERT: F 822 MET cc_start: 0.8235 (pmm) cc_final: 0.7775 (pp-130) REVERT: E 51 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: E 184 PHE cc_start: 0.8637 (p90) cc_final: 0.7824 (p90) REVERT: E 325 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.6942 (t80) REVERT: E 346 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9119 (mt) REVERT: E 397 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7597 (t80) REVERT: E 634 MET cc_start: -0.0268 (tpt) cc_final: -0.0797 (tpp) outliers start: 165 outliers final: 88 residues processed: 367 average time/residue: 0.5045 time to fit residues: 233.8147 Evaluate side-chains 341 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 219 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 397 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [118, 75, 356, 408, 66, 271, 205, 332, 133, 123, 345] chunk 118 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 356 optimal weight: 0.6980 chunk 408 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS D 538 HIS F 51 GLN ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.134432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081921 restraints weight = 181234.543| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.93 r_work: 0.2967 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35160 Z= 0.183 Angle : 0.644 16.738 47622 Z= 0.315 Chirality : 0.043 0.170 5532 Planarity : 0.004 0.044 5892 Dihedral : 7.130 59.739 4598 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.64 % Rotamer: Outliers : 4.35 % Allowed : 14.35 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 4182 helix: 0.12 (0.12), residues: 1879 sheet: -1.59 (0.23), residues: 615 loop : -0.20 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 812 TYR 0.019 0.001 TYR A 167 PHE 0.030 0.002 PHE D 165 TRP 0.037 0.001 TRP F 555 HIS 0.007 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (35148) covalent geometry : angle 0.64355 / 0.31 (47598) SS BOND : bond 0.00905 / 0.55 ( 12) SS BOND : angle 1.44952 / 1.05 ( 24) hydrogen bonds : bond 0.04109 / 2.70 ( 1442) hydrogen bonds : angle 4.47360 / 3.18 ( 3543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 219 time to evaluate : 0.971 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: A 27 PHE cc_start: 0.8314 (t80) cc_final: 0.7799 (m-10) REVERT: A 37 MET cc_start: 0.8808 (tmm) cc_final: 0.8523 (tmt) REVERT: A 51 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: A 53 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9161 (m) REVERT: A 165 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8268 (t80) REVERT: A 177 MET cc_start: 0.9215 (mmm) cc_final: 0.8867 (mtp) REVERT: A 355 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9257 (t) REVERT: A 390 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 397 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: A 408 ASP cc_start: 0.8269 (t0) cc_final: 0.7899 (t70) REVERT: A 409 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7601 (mm) REVERT: A 422 MET cc_start: 0.9333 (mmm) cc_final: 0.8978 (mmm) REVERT: A 448 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 463 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8611 (t-90) REVERT: A 477 PHE cc_start: 0.9025 (t80) cc_final: 0.8814 (t80) REVERT: A 478 MET cc_start: 0.8856 (mmm) cc_final: 0.8613 (mmm) REVERT: A 635 MET cc_start: 0.8547 (pmm) cc_final: 0.8309 (pmm) REVERT: A 784 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: A 822 MET cc_start: 0.8757 (ptp) cc_final: 0.8114 (pmm) REVERT: C 37 MET cc_start: 0.9359 (mtm) cc_final: 0.8882 (ttp) REVERT: C 194 GLU cc_start: 0.8501 (pp20) cc_final: 0.8282 (pp20) REVERT: C 287 LEU cc_start: 0.9280 (mp) cc_final: 0.9065 (tp) REVERT: C 355 THR cc_start: 0.9666 (OUTLIER) cc_final: 0.9289 (t) REVERT: C 390 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8541 (pp) REVERT: C 414 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7857 (p0) REVERT: C 473 GLU cc_start: 0.8980 (tt0) cc_final: 0.8499 (tm-30) REVERT: C 477 PHE cc_start: 0.8721 (t80) cc_final: 0.8506 (t80) REVERT: C 509 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7767 (pp) REVERT: C 517 GLU cc_start: 0.7807 (mp0) cc_final: 0.7507 (mp0) REVERT: C 578 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6312 (mmp) REVERT: C 635 MET cc_start: 0.8844 (pmt) cc_final: 0.8626 (pmm) REVERT: C 712 TYR cc_start: 0.9313 (m-80) cc_final: 0.8943 (m-10) REVERT: B 40 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8732 (tp) REVERT: B 165 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7902 (t80) REVERT: B 194 GLU cc_start: 0.9081 (tp30) cc_final: 0.8663 (tm-30) REVERT: B 202 LYS cc_start: 0.9058 (mttm) cc_final: 0.8788 (mtmt) REVERT: B 205 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8626 (pp20) REVERT: B 319 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7944 (t80) REVERT: B 325 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.5582 (t80) REVERT: B 378 PHE cc_start: 0.9089 (m-80) cc_final: 0.8578 (m-10) REVERT: B 478 MET cc_start: 0.8974 (mmm) cc_final: 0.8767 (mmm) REVERT: B 498 GLU cc_start: 0.9200 (tt0) cc_final: 0.8891 (tp30) REVERT: B 508 LYS cc_start: 0.9183 (tttp) cc_final: 0.8764 (tppt) REVERT: B 511 GLN cc_start: 0.9132 (tt0) cc_final: 0.8866 (tt0) REVERT: B 562 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8563 (tm) REVERT: B 578 MET cc_start: 0.5972 (mpp) cc_final: 0.5423 (mmt) REVERT: B 652 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: B 790 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (tm) REVERT: B 804 GLU cc_start: 0.8183 (tt0) cc_final: 0.7874 (pt0) REVERT: B 822 MET cc_start: 0.8140 (ptp) cc_final: 0.7503 (pmm) REVERT: D 17 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7223 (p90) REVERT: D 18 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8008 (mmm160) REVERT: D 202 LYS cc_start: 0.9122 (mttm) cc_final: 0.8903 (mmpt) REVERT: D 283 GLN cc_start: 0.9493 (mm-40) cc_final: 0.8946 (mm-40) REVERT: D 319 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7954 (t80) REVERT: D 361 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8777 (tpp) REVERT: D 397 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 555 TRP cc_start: 0.6638 (p-90) cc_final: 0.6105 (p90) REVERT: D 635 MET cc_start: 0.7304 (mmm) cc_final: 0.6483 (pmm) REVERT: F 27 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7697 (m-10) REVERT: F 165 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: F 192 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5877 (mttp) REVERT: F 325 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6871 (t80) REVERT: F 416 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5987 (t80) REVERT: F 420 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8275 (tp) REVERT: F 615 LYS cc_start: 0.9063 (tttt) cc_final: 0.8801 (mptt) REVERT: F 782 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8570 (tm) REVERT: F 790 LEU cc_start: 0.8720 (pt) cc_final: 0.8294 (tm) REVERT: F 822 MET cc_start: 0.8372 (pmm) cc_final: 0.7959 (pp-130) REVERT: E 51 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8888 (pm20) REVERT: E 184 PHE cc_start: 0.8654 (p90) cc_final: 0.7878 (p90) REVERT: E 325 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.6995 (t80) REVERT: E 346 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9076 (mt) REVERT: E 390 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8054 (pp) REVERT: E 397 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7551 (t80) outliers start: 169 outliers final: 97 residues processed: 351 average time/residue: 0.5360 time to fit residues: 237.1929 Evaluate side-chains 346 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 212 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [334, 133, 406, 18, 125, 190, 357, 284, 335, 13, 123] chunk 334 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 406 optimal weight: 40.0000 chunk 18 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 357 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 GLN F 51 GLN ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 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 = 0.4362 r_free = 0.4362 target = 0.132653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.077289 restraints weight = 160732.337| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.13 r_work: 0.3051 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35160 Z= 0.171 Angle : 0.639 14.878 47622 Z= 0.312 Chirality : 0.043 0.229 5532 Planarity : 0.004 0.043 5892 Dihedral : 7.080 59.588 4594 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.64 % Rotamer: Outliers : 4.22 % Allowed : 14.94 % Favored : 80.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 4182 helix: 0.22 (0.12), residues: 1868 sheet: -1.59 (0.22), residues: 614 loop : -0.18 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 649 TYR 0.019 0.001 TYR A 167 PHE 0.028 0.002 PHE D 165 TRP 0.037 0.001 TRP F 555 HIS 0.006 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (35148) covalent geometry : angle 0.63834 / 0.31 (47598) SS BOND : bond 0.00785 / 0.44 ( 12) SS BOND : angle 1.33855 / 0.98 ( 24) hydrogen bonds : bond 0.03975 / 2.61 ( 1442) hydrogen bonds : angle 4.35684 / 3.08 ( 3543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 221 time to evaluate : 1.525 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: A 27 PHE cc_start: 0.8279 (t80) cc_final: 0.7758 (m-10) REVERT: A 37 MET cc_start: 0.8803 (tmm) cc_final: 0.8467 (tmt) REVERT: A 51 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: A 53 VAL cc_start: 0.9530 (OUTLIER) cc_final: 0.9185 (m) REVERT: A 165 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 177 MET cc_start: 0.9175 (mmm) cc_final: 0.8806 (mtp) REVERT: A 355 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9283 (t) REVERT: A 390 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 397 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: A 408 ASP cc_start: 0.8067 (t0) cc_final: 0.7756 (t70) REVERT: A 409 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 422 MET cc_start: 0.9301 (mmm) cc_final: 0.8923 (mmm) REVERT: A 448 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 463 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8507 (t-90) REVERT: A 635 MET cc_start: 0.8522 (pmm) cc_final: 0.8275 (pmm) REVERT: A 784 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: A 822 MET cc_start: 0.8868 (ptp) cc_final: 0.8119 (pmm) REVERT: C 37 MET cc_start: 0.9272 (mtm) cc_final: 0.8880 (ttp) REVERT: C 165 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 287 LEU cc_start: 0.9292 (mp) cc_final: 0.9083 (tp) REVERT: C 390 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (pp) REVERT: C 414 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (p0) REVERT: C 473 GLU cc_start: 0.8944 (tt0) cc_final: 0.8465 (tm-30) REVERT: C 509 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7709 (pp) REVERT: C 517 GLU cc_start: 0.7854 (mp0) cc_final: 0.7547 (mp0) REVERT: C 578 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5964 (mmp) REVERT: C 634 MET cc_start: 0.6485 (mmt) cc_final: 0.6257 (mmt) REVERT: C 635 MET cc_start: 0.8758 (pmt) cc_final: 0.8463 (pmm) REVERT: C 712 TYR cc_start: 0.9304 (m-80) cc_final: 0.8866 (m-10) REVERT: C 757 LEU cc_start: 0.9810 (tt) cc_final: 0.9594 (mt) REVERT: B 40 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8762 (tp) REVERT: B 165 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 177 MET cc_start: 0.9184 (tpp) cc_final: 0.8982 (mmt) REVERT: B 194 GLU cc_start: 0.9035 (tp30) cc_final: 0.8545 (tm-30) REVERT: B 202 LYS cc_start: 0.9063 (mttm) cc_final: 0.8774 (mtmt) REVERT: B 205 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8590 (pp20) REVERT: B 319 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 325 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.5523 (t80) REVERT: B 378 PHE cc_start: 0.9072 (m-80) cc_final: 0.8551 (m-10) REVERT: B 478 MET cc_start: 0.8888 (mmm) cc_final: 0.8639 (mmm) REVERT: B 498 GLU cc_start: 0.9096 (tt0) cc_final: 0.8802 (tp30) REVERT: B 508 LYS cc_start: 0.9217 (tttp) cc_final: 0.8838 (tppt) REVERT: B 562 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8572 (tm) REVERT: B 578 MET cc_start: 0.5908 (mpp) cc_final: 0.5383 (mmt) REVERT: B 635 MET cc_start: 0.8863 (pmm) cc_final: 0.8480 (pmm) REVERT: B 652 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6691 (t-90) REVERT: B 804 GLU cc_start: 0.8105 (tt0) cc_final: 0.7830 (pt0) REVERT: D 17 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7192 (p90) REVERT: D 18 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8053 (mmm160) REVERT: D 202 LYS cc_start: 0.9162 (mttm) cc_final: 0.8821 (mmtm) REVERT: D 283 GLN cc_start: 0.9490 (mm-40) cc_final: 0.8939 (mm-40) REVERT: D 319 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7912 (t80) REVERT: D 361 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8640 (tpp) REVERT: D 397 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: D 555 TRP cc_start: 0.6651 (p-90) cc_final: 0.6082 (p90) REVERT: D 635 MET cc_start: 0.7419 (mmm) cc_final: 0.6635 (pmm) REVERT: F 27 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: F 28 MET cc_start: 0.8086 (tpp) cc_final: 0.7777 (mmm) REVERT: F 165 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: F 192 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.5902 (mttp) REVERT: F 287 LEU cc_start: 0.8307 (mm) cc_final: 0.7838 (tm) REVERT: F 294 PHE cc_start: 0.6247 (t80) cc_final: 0.5945 (t80) REVERT: F 319 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7034 (t80) REVERT: F 416 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5760 (t80) REVERT: F 615 LYS cc_start: 0.9078 (tttt) cc_final: 0.8779 (mptt) REVERT: F 673 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5525 (mm) REVERT: F 782 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8535 (tm) REVERT: F 813 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8178 (mm) REVERT: F 822 MET cc_start: 0.8289 (pmm) cc_final: 0.7838 (pp-130) REVERT: E 51 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.9002 (pm20) REVERT: E 325 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6980 (t80) REVERT: E 346 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9146 (mt) REVERT: E 397 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7533 (t80) REVERT: E 420 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (mt) REVERT: E 555 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7507 (m-10) outliers start: 164 outliers final: 98 residues processed: 345 average time/residue: 0.5140 time to fit residues: 224.8078 Evaluate side-chains 348 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 212 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain F residue 813 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 555 TRP Chi-restraints excluded: chain E residue 578 MET Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [6, 4, 208, 126, 387, 369, 417, 313, 67, 249, 279] chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 417 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 ASN D 516 GLN F 51 GLN F 475 HIS ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076944 restraints weight = 151196.249| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.97 r_work: 0.3047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 35160 Z= 0.193 Angle : 0.652 14.459 47622 Z= 0.319 Chirality : 0.044 0.265 5532 Planarity : 0.004 0.044 5892 Dihedral : 7.133 59.454 4594 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 4.10 % Allowed : 15.22 % Favored : 80.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 4182 helix: 0.20 (0.12), residues: 1871 sheet: -1.60 (0.22), residues: 613 loop : -0.21 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 821 TYR 0.019 0.002 TYR A 167 PHE 0.029 0.002 PHE D 165 TRP 0.036 0.001 TRP F 555 HIS 0.009 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (35148) covalent geometry : angle 0.65106 / 0.32 (47598) SS BOND : bond 0.00774 / 0.46 ( 12) SS BOND : angle 1.36935 / 1.00 ( 24) hydrogen bonds : bond 0.03966 / 2.60 ( 1442) hydrogen bonds : angle 4.35370 / 3.08 ( 3543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 216 time to evaluate : 1.151 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: A 27 PHE cc_start: 0.8302 (t80) cc_final: 0.7774 (m-10) REVERT: A 37 MET cc_start: 0.8813 (tmm) cc_final: 0.8475 (tmt) REVERT: A 50 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8809 (t0) REVERT: A 51 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: A 53 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9174 (m) REVERT: A 165 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8107 (t80) REVERT: A 177 MET cc_start: 0.9065 (mmm) cc_final: 0.8691 (mtp) REVERT: A 355 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9296 (t) REVERT: A 390 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 397 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: A 408 ASP cc_start: 0.8084 (t0) cc_final: 0.7771 (t70) REVERT: A 409 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 422 MET cc_start: 0.9294 (mmm) cc_final: 0.8908 (mmm) REVERT: A 448 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 463 HIS cc_start: 0.9068 (OUTLIER) cc_final: 0.8498 (t-90) REVERT: A 477 PHE cc_start: 0.9009 (t80) cc_final: 0.8560 (t80) REVERT: A 499 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8971 (OUTLIER) REVERT: A 635 MET cc_start: 0.8418 (pmm) cc_final: 0.8183 (pmm) REVERT: A 784 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: A 822 MET cc_start: 0.8856 (ptp) cc_final: 0.8055 (pmm) REVERT: C 37 MET cc_start: 0.9269 (mtm) cc_final: 0.8875 (ttp) REVERT: C 165 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 390 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8553 (pp) REVERT: C 414 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (p0) REVERT: C 473 GLU cc_start: 0.8972 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 477 PHE cc_start: 0.8720 (t80) cc_final: 0.8363 (t80) REVERT: C 484 ASP cc_start: 0.8553 (p0) cc_final: 0.8352 (t0) REVERT: C 509 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7821 (pp) REVERT: C 517 GLU cc_start: 0.7846 (mp0) cc_final: 0.7512 (mp0) REVERT: C 578 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5851 (mmp) REVERT: C 634 MET cc_start: 0.6497 (mmt) cc_final: 0.6256 (mmt) REVERT: C 635 MET cc_start: 0.8771 (pmt) cc_final: 0.8500 (pmm) REVERT: C 712 TYR cc_start: 0.9301 (m-80) cc_final: 0.8803 (m-10) REVERT: C 757 LEU cc_start: 0.9794 (tt) cc_final: 0.9560 (mt) REVERT: C 822 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5711 (ppp) REVERT: B 40 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8770 (tp) REVERT: B 165 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (t80) REVERT: B 194 GLU cc_start: 0.9024 (tp30) cc_final: 0.8535 (tm-30) REVERT: B 202 LYS cc_start: 0.9060 (mttm) cc_final: 0.8765 (mtmt) REVERT: B 205 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8561 (pp20) REVERT: B 319 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 325 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5434 (t80) REVERT: B 378 PHE cc_start: 0.9077 (m-80) cc_final: 0.8579 (m-10) REVERT: B 478 MET cc_start: 0.8873 (mmm) cc_final: 0.8628 (mmm) REVERT: B 498 GLU cc_start: 0.9071 (tt0) cc_final: 0.8794 (tp30) REVERT: B 508 LYS cc_start: 0.9191 (tttp) cc_final: 0.8857 (tppt) REVERT: B 562 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8556 (tm) REVERT: B 578 MET cc_start: 0.5889 (mpp) cc_final: 0.5382 (mmt) REVERT: B 652 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6602 (t-90) REVERT: B 790 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8760 (tm) REVERT: B 804 GLU cc_start: 0.8094 (tt0) cc_final: 0.7793 (pt0) REVERT: D 17 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7186 (p90) REVERT: D 18 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8119 (mmm160) REVERT: D 283 GLN cc_start: 0.9498 (mm-40) cc_final: 0.8936 (mm-40) REVERT: D 361 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8563 (tpp) REVERT: D 397 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: D 555 TRP cc_start: 0.6733 (p-90) cc_final: 0.6175 (p90) REVERT: D 635 MET cc_start: 0.7339 (mmm) cc_final: 0.6491 (pmm) REVERT: F 27 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: F 28 MET cc_start: 0.8013 (tpp) cc_final: 0.7754 (mmm) REVERT: F 165 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7909 (m-10) REVERT: F 192 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.5959 (mttp) REVERT: F 287 LEU cc_start: 0.8354 (mm) cc_final: 0.7935 (tm) REVERT: F 325 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.6857 (t80) REVERT: F 416 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5656 (t80) REVERT: F 420 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8306 (tp) REVERT: F 615 LYS cc_start: 0.9090 (tttt) cc_final: 0.8768 (mptt) REVERT: F 673 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5405 (mm) REVERT: F 782 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8522 (tm) REVERT: F 790 LEU cc_start: 0.8878 (pt) cc_final: 0.8342 (tm) REVERT: F 822 MET cc_start: 0.8255 (pmm) cc_final: 0.7784 (pp-130) REVERT: E 51 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: E 325 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.6988 (t80) REVERT: E 346 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9130 (mt) REVERT: E 397 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7539 (t80) REVERT: E 420 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8595 (mt) REVERT: E 555 TRP cc_start: 0.7790 (m-10) cc_final: 0.7454 (m-10) REVERT: E 634 MET cc_start: -0.0978 (tpp) cc_final: -0.2098 (tmm) outliers start: 159 outliers final: 101 residues processed: 340 average time/residue: 0.5182 time to fit residues: 222.1672 Evaluate side-chains 348 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 208 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 578 MET Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [19, 290, 22, 310, 137, 363, 337, 96, 27, 415, 63] chunk 19 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 310 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 363 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 415 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN F 51 GLN ** F 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 847 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.132876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078003 restraints weight = 130560.937| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.73 r_work: 0.3081 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35160 Z= 0.146 Angle : 0.639 13.716 47622 Z= 0.311 Chirality : 0.043 0.244 5532 Planarity : 0.004 0.043 5892 Dihedral : 7.070 59.665 4594 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer: Outliers : 3.97 % Allowed : 15.50 % Favored : 80.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 4182 helix: 0.27 (0.12), residues: 1872 sheet: -1.59 (0.22), residues: 614 loop : -0.19 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 466 TYR 0.017 0.001 TYR A 167 PHE 0.036 0.001 PHE F 679 TRP 0.041 0.002 TRP D 691 HIS 0.008 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (35148) covalent geometry : angle 0.63861 / 0.31 (47598) SS BOND : bond 0.00604 / 0.35 ( 12) SS BOND : angle 1.17450 / 0.87 ( 24) hydrogen bonds : bond 0.03840 / 2.51 ( 1442) hydrogen bonds : angle 4.21405 / 2.98 ( 3543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 223 time to evaluate : 1.235 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: A 27 PHE cc_start: 0.8276 (t80) cc_final: 0.7753 (m-10) REVERT: A 37 MET cc_start: 0.8780 (tmm) cc_final: 0.8437 (tmt) REVERT: A 50 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8799 (t0) REVERT: A 51 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8683 (pm20) REVERT: A 53 VAL cc_start: 0.9536 (OUTLIER) cc_final: 0.9189 (m) REVERT: A 165 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 177 MET cc_start: 0.9167 (mmm) cc_final: 0.8787 (mtp) REVERT: A 183 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (p-90) REVERT: A 336 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: A 355 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9272 (t) REVERT: A 390 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 397 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: A 408 ASP cc_start: 0.8016 (t0) cc_final: 0.7710 (t70) REVERT: A 409 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7597 (mm) REVERT: A 422 MET cc_start: 0.9293 (mmm) cc_final: 0.9028 (mmm) REVERT: A 448 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 463 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8478 (t-90) REVERT: A 477 PHE cc_start: 0.8669 (t80) cc_final: 0.8277 (t80) REVERT: A 478 MET cc_start: 0.8268 (mmm) cc_final: 0.8033 (mmp) REVERT: A 784 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: A 822 MET cc_start: 0.8864 (ptp) cc_final: 0.8162 (pmm) REVERT: C 37 MET cc_start: 0.9227 (mtm) cc_final: 0.8860 (ttp) REVERT: C 165 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8044 (t80) REVERT: C 355 THR cc_start: 0.9595 (OUTLIER) cc_final: 0.9240 (t) REVERT: C 390 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8547 (pp) REVERT: C 414 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7964 (p0) REVERT: C 473 GLU cc_start: 0.8949 (tt0) cc_final: 0.8459 (tm-30) REVERT: C 477 PHE cc_start: 0.8684 (t80) cc_final: 0.8277 (t80) REVERT: C 484 ASP cc_start: 0.8543 (p0) cc_final: 0.8318 (t0) REVERT: C 509 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7768 (pp) REVERT: C 517 GLU cc_start: 0.7814 (mp0) cc_final: 0.7504 (mp0) REVERT: C 578 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5777 (mmp) REVERT: C 634 MET cc_start: 0.6542 (mmt) cc_final: 0.6318 (mmt) REVERT: C 635 MET cc_start: 0.8775 (pmt) cc_final: 0.8521 (pmm) REVERT: C 712 TYR cc_start: 0.9307 (m-80) cc_final: 0.8806 (m-10) REVERT: C 757 LEU cc_start: 0.9803 (tt) cc_final: 0.9585 (mt) REVERT: C 822 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6208 (ppp) REVERT: B 40 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 165 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 194 GLU cc_start: 0.9004 (tp30) cc_final: 0.8514 (tm-30) REVERT: B 202 LYS cc_start: 0.9080 (mttm) cc_final: 0.8771 (mtmt) REVERT: B 205 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8541 (pp20) REVERT: B 319 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 325 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.5305 (t80) REVERT: B 378 PHE cc_start: 0.9076 (m-80) cc_final: 0.8574 (m-10) REVERT: B 478 MET cc_start: 0.8867 (mmm) cc_final: 0.8616 (mmm) REVERT: B 498 GLU cc_start: 0.9046 (tt0) cc_final: 0.8768 (tp30) REVERT: B 508 LYS cc_start: 0.9172 (tttp) cc_final: 0.8820 (tppt) REVERT: B 511 GLN cc_start: 0.9096 (tt0) cc_final: 0.8857 (tt0) REVERT: B 562 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8567 (tm) REVERT: B 578 MET cc_start: 0.5872 (mpp) cc_final: 0.5382 (mmt) REVERT: B 635 MET cc_start: 0.8927 (pmm) cc_final: 0.8534 (pmm) REVERT: B 652 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6752 (t-90) REVERT: B 790 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8755 (tm) REVERT: B 804 GLU cc_start: 0.7992 (tt0) cc_final: 0.7713 (pt0) REVERT: D 319 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7887 (t80) REVERT: D 361 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8604 (tpp) REVERT: D 397 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: D 555 TRP cc_start: 0.6782 (p-90) cc_final: 0.6230 (p90) REVERT: D 635 MET cc_start: 0.7429 (mmm) cc_final: 0.6644 (pmm) REVERT: D 822 MET cc_start: 0.2273 (mmm) cc_final: 0.1958 (pp-130) REVERT: F 27 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7759 (m-10) REVERT: F 28 MET cc_start: 0.8005 (tpp) cc_final: 0.7753 (mmm) REVERT: F 165 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: F 192 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5920 (mttp) REVERT: F 287 LEU cc_start: 0.8367 (mm) cc_final: 0.7976 (tm) REVERT: F 319 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7008 (t80) REVERT: F 416 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5810 (t80) REVERT: F 420 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8277 (tp) REVERT: F 484 ASP cc_start: 0.8084 (p0) cc_final: 0.7643 (p0) REVERT: F 615 LYS cc_start: 0.9040 (tttt) cc_final: 0.8695 (mptt) REVERT: F 782 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8587 (tm) REVERT: F 790 LEU cc_start: 0.8860 (pt) cc_final: 0.8363 (tm) REVERT: F 804 GLU cc_start: 0.8575 (tt0) cc_final: 0.7963 (tp30) REVERT: F 822 MET cc_start: 0.8298 (pmm) cc_final: 0.7846 (pp-130) REVERT: E 325 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6888 (t80) REVERT: E 346 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9112 (mt) REVERT: E 397 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7519 (t80) REVERT: E 454 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: E 555 TRP cc_start: 0.7868 (m-10) cc_final: 0.7536 (m-10) REVERT: E 634 MET cc_start: -0.0572 (tpp) cc_final: -0.2037 (tmm) outliers start: 154 outliers final: 99 residues processed: 343 average time/residue: 0.5047 time to fit residues: 220.6820 Evaluate side-chains 351 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 212 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 782 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 578 MET Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [128, 392, 268, 346, 275, 406, 358, 60, 304, 151, 81] chunk 128 optimal weight: 30.0000 chunk 392 optimal weight: 50.0000 chunk 268 optimal weight: 1.9990 chunk 346 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 304 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN ** F 770 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 = 0.4366 r_free = 0.4366 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080811 restraints weight = 190839.026| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.52 r_work: 0.3009 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35160 Z= 0.155 Angle : 0.641 14.081 47622 Z= 0.312 Chirality : 0.043 0.224 5532 Planarity : 0.004 0.043 5892 Dihedral : 7.038 59.984 4593 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.55 % Rotamer: Outliers : 3.82 % Allowed : 16.03 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 4182 helix: 0.26 (0.12), residues: 1874 sheet: -1.60 (0.22), residues: 615 loop : -0.17 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 671 TYR 0.017 0.001 TYR A 167 PHE 0.030 0.001 PHE F 679 TRP 0.040 0.001 TRP F 555 HIS 0.015 0.001 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (35148) covalent geometry : angle 0.64081 / 0.31 (47598) SS BOND : bond 0.00593 / 0.35 ( 12) SS BOND : angle 1.18958 / 0.88 ( 24) hydrogen bonds : bond 0.03808 / 2.48 ( 1442) hydrogen bonds : angle 4.21813 / 2.98 ( 3543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 215 time to evaluate : 1.234 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: A 27 PHE cc_start: 0.8311 (t80) cc_final: 0.7798 (m-10) REVERT: A 37 MET cc_start: 0.8833 (tmm) cc_final: 0.8486 (tmt) REVERT: A 51 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 53 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9154 (m) REVERT: A 165 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 177 MET cc_start: 0.9053 (mmm) cc_final: 0.8702 (mtp) REVERT: A 183 TRP cc_start: 0.8720 (OUTLIER) cc_final: 0.8489 (p-90) REVERT: A 336 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8803 (pm20) REVERT: A 355 THR cc_start: 0.9508 (OUTLIER) cc_final: 0.9259 (t) REVERT: A 390 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 397 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: A 408 ASP cc_start: 0.8167 (t0) cc_final: 0.7819 (t70) REVERT: A 409 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7596 (mm) REVERT: A 422 MET cc_start: 0.9314 (mmm) cc_final: 0.9046 (mmm) REVERT: A 448 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 463 HIS cc_start: 0.9146 (OUTLIER) cc_final: 0.8556 (t-90) REVERT: A 784 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: A 822 MET cc_start: 0.8815 (ptp) cc_final: 0.8059 (pmm) REVERT: C 37 MET cc_start: 0.9321 (mtm) cc_final: 0.8838 (ttt) REVERT: C 165 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8017 (t80) REVERT: C 355 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9225 (t) REVERT: C 390 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8451 (pp) REVERT: C 414 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7918 (p0) REVERT: C 473 GLU cc_start: 0.8946 (tt0) cc_final: 0.8438 (tm-30) REVERT: C 477 PHE cc_start: 0.8816 (t80) cc_final: 0.8362 (t80) REVERT: C 484 ASP cc_start: 0.8759 (p0) cc_final: 0.8297 (t0) REVERT: C 509 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7847 (pp) REVERT: C 517 GLU cc_start: 0.7867 (mp0) cc_final: 0.7607 (mp0) REVERT: C 578 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6016 (mmp) REVERT: C 635 MET cc_start: 0.8806 (pmt) cc_final: 0.8554 (pmm) REVERT: C 712 TYR cc_start: 0.9232 (m-80) cc_final: 0.8806 (m-10) REVERT: C 822 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6121 (ppp) REVERT: B 40 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 45 MET cc_start: 0.9293 (tpp) cc_final: 0.9085 (mmt) REVERT: B 165 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 194 GLU cc_start: 0.9048 (tp30) cc_final: 0.8551 (tm-30) REVERT: B 202 LYS cc_start: 0.9062 (mttm) cc_final: 0.8775 (mtmt) REVERT: B 205 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8558 (pp20) REVERT: B 319 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7777 (t80) REVERT: B 325 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5363 (t80) REVERT: B 378 PHE cc_start: 0.9100 (m-80) cc_final: 0.8579 (m-10) REVERT: B 478 MET cc_start: 0.8942 (mmm) cc_final: 0.8661 (mmm) REVERT: B 498 GLU cc_start: 0.9143 (tt0) cc_final: 0.8801 (tp30) REVERT: B 508 LYS cc_start: 0.9139 (tttp) cc_final: 0.8754 (tppt) REVERT: B 511 GLN cc_start: 0.9131 (tt0) cc_final: 0.8864 (tt0) REVERT: B 562 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8473 (tm) REVERT: B 578 MET cc_start: 0.6180 (mpp) cc_final: 0.5716 (mmt) REVERT: B 635 MET cc_start: 0.8990 (pmm) cc_final: 0.8594 (pmm) REVERT: B 652 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6910 (t-90) REVERT: B 790 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8761 (tm) REVERT: B 804 GLU cc_start: 0.8030 (tt0) cc_final: 0.7740 (pt0) REVERT: D 18 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8257 (mmm160) REVERT: D 319 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7882 (t80) REVERT: D 361 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8681 (tpp) REVERT: D 397 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: D 555 TRP cc_start: 0.6833 (p-90) cc_final: 0.6291 (p90) REVERT: D 635 MET cc_start: 0.7404 (mmm) cc_final: 0.6550 (pmm) REVERT: F 27 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: F 28 MET cc_start: 0.7940 (tpp) cc_final: 0.7685 (mmm) REVERT: F 165 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7891 (t80) REVERT: F 192 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.5856 (mttp) REVERT: F 287 LEU cc_start: 0.8367 (mm) cc_final: 0.7972 (tm) REVERT: F 319 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6968 (t80) REVERT: F 416 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.5888 (t80) REVERT: F 420 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8297 (tp) REVERT: F 484 ASP cc_start: 0.8041 (p0) cc_final: 0.7629 (p0) REVERT: F 615 LYS cc_start: 0.9038 (tttt) cc_final: 0.8705 (mptt) REVERT: F 782 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (tm) REVERT: F 790 LEU cc_start: 0.8803 (pt) cc_final: 0.8235 (tm) REVERT: F 804 GLU cc_start: 0.8571 (tt0) cc_final: 0.7980 (tp30) REVERT: F 822 MET cc_start: 0.8353 (pmm) cc_final: 0.7922 (pp-130) REVERT: E 325 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.6896 (t80) REVERT: E 346 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9066 (mt) REVERT: E 397 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7499 (t80) REVERT: E 420 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 454 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: E 555 TRP cc_start: 0.7796 (m-10) cc_final: 0.7494 (m-10) REVERT: E 634 MET cc_start: -0.1852 (tpp) cc_final: -0.3033 (tmm) outliers start: 148 outliers final: 98 residues processed: 328 average time/residue: 0.5365 time to fit residues: 223.8884 Evaluate side-chains 345 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 207 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 416 PHE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 578 MET Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [413, 146, 11, 382, 361, 2, 193, 388, 379, 273, 362] chunk 413 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 382 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 193 optimal weight: 0.0040 chunk 388 optimal weight: 20.0000 chunk 379 optimal weight: 0.9990 chunk 273 optimal weight: 20.0000 chunk 362 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN ** F 770 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 = 0.4380 r_free = 0.4380 target = 0.135969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083443 restraints weight = 157389.553| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.82 r_work: 0.3056 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35160 Z= 0.116 Angle : 0.637 14.353 47622 Z= 0.306 Chirality : 0.042 0.216 5532 Planarity : 0.004 0.042 5892 Dihedral : 6.872 59.827 4591 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.54 % Allowed : 16.36 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 4182 helix: 0.33 (0.12), residues: 1880 sheet: -1.56 (0.22), residues: 617 loop : -0.11 (0.17), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 821 TYR 0.016 0.001 TYR F 566 PHE 0.028 0.001 PHE F 679 TRP 0.043 0.002 TRP F 555 HIS 0.004 0.001 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (35148) covalent geometry : angle 0.63660 / 0.31 (47598) SS BOND : bond 0.00399 / 0.23 ( 12) SS BOND : angle 1.01081 / 0.75 ( 24) hydrogen bonds : bond 0.03631 / 2.38 ( 1442) hydrogen bonds : angle 4.07262 / 2.87 ( 3543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 229 time to evaluate : 1.280 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: A 27 PHE cc_start: 0.8257 (t80) cc_final: 0.7734 (m-10) REVERT: A 37 MET cc_start: 0.8806 (tmm) cc_final: 0.8450 (tmt) REVERT: A 51 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: A 53 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9178 (m) REVERT: A 165 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7954 (t80) REVERT: A 177 MET cc_start: 0.9040 (mmm) cc_final: 0.8678 (mtp) REVERT: A 355 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9185 (t) REVERT: A 390 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8727 (pp) REVERT: A 397 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: A 408 ASP cc_start: 0.8087 (t0) cc_final: 0.7761 (t70) REVERT: A 409 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7594 (mm) REVERT: A 422 MET cc_start: 0.9413 (mmm) cc_final: 0.9147 (mmm) REVERT: A 448 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 463 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8525 (t-90) REVERT: A 822 MET cc_start: 0.8872 (ptp) cc_final: 0.8239 (pmm) REVERT: C 37 MET cc_start: 0.9334 (mtm) cc_final: 0.8847 (ttp) REVERT: C 165 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7993 (t80) REVERT: C 285 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9143 (ptmt) REVERT: C 355 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9190 (t) REVERT: C 390 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8445 (pp) REVERT: C 414 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7780 (p0) REVERT: C 473 GLU cc_start: 0.8932 (tt0) cc_final: 0.8432 (tm-30) REVERT: C 477 PHE cc_start: 0.8839 (t80) cc_final: 0.8398 (t80) REVERT: C 484 ASP cc_start: 0.8720 (p0) cc_final: 0.8092 (t0) REVERT: C 509 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7790 (pp) REVERT: C 517 GLU cc_start: 0.7832 (mp0) cc_final: 0.7555 (mp0) REVERT: C 578 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5922 (mmp) REVERT: C 635 MET cc_start: 0.8747 (pmt) cc_final: 0.8507 (pmm) REVERT: C 712 TYR cc_start: 0.9220 (m-80) cc_final: 0.8743 (m-10) REVERT: C 822 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5792 (ppp) REVERT: B 35 MET cc_start: 0.8818 (ttm) cc_final: 0.8607 (mtp) REVERT: B 40 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 47 LEU cc_start: 0.9125 (tt) cc_final: 0.8864 (mt) REVERT: B 165 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7666 (t80) REVERT: B 194 GLU cc_start: 0.9042 (tp30) cc_final: 0.8654 (mm-30) REVERT: B 202 LYS cc_start: 0.9043 (mttm) cc_final: 0.8750 (mtpt) REVERT: B 205 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8501 (pp20) REVERT: B 319 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 325 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5341 (t80) REVERT: B 378 PHE cc_start: 0.9075 (m-80) cc_final: 0.8575 (m-10) REVERT: B 478 MET cc_start: 0.8875 (mmm) cc_final: 0.8568 (mmm) REVERT: B 498 GLU cc_start: 0.9125 (tt0) cc_final: 0.8778 (tp30) REVERT: B 508 LYS cc_start: 0.9099 (tttp) cc_final: 0.8707 (tppt) REVERT: B 511 GLN cc_start: 0.9079 (tt0) cc_final: 0.8752 (tt0) REVERT: B 562 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8466 (tm) REVERT: B 578 MET cc_start: 0.6173 (mpp) cc_final: 0.5720 (mmt) REVERT: B 590 LEU cc_start: 0.9347 (tp) cc_final: 0.8939 (tm) REVERT: B 635 MET cc_start: 0.8945 (pmm) cc_final: 0.8529 (pmm) REVERT: B 790 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8772 (tm) REVERT: B 804 GLU cc_start: 0.8003 (tt0) cc_final: 0.7741 (pt0) REVERT: D 18 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8248 (mmm160) REVERT: D 290 LYS cc_start: 0.9003 (tppp) cc_final: 0.8659 (tppt) REVERT: D 319 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (t80) REVERT: D 361 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8677 (tpp) REVERT: D 397 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: D 555 TRP cc_start: 0.6882 (p-90) cc_final: 0.6180 (p90) REVERT: D 635 MET cc_start: 0.7366 (mmm) cc_final: 0.6473 (pmm) REVERT: D 822 MET cc_start: 0.4358 (ppp) cc_final: 0.3856 (mmm) REVERT: F 27 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: F 28 MET cc_start: 0.8018 (tpp) cc_final: 0.7731 (mmm) REVERT: F 29 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7986 (p0) REVERT: F 165 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7882 (t80) REVERT: F 287 LEU cc_start: 0.8207 (mm) cc_final: 0.7857 (tm) REVERT: F 319 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6840 (t80) REVERT: F 420 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (tp) REVERT: F 484 ASP cc_start: 0.8014 (p0) cc_final: 0.7593 (p0) REVERT: F 615 LYS cc_start: 0.9045 (tttt) cc_final: 0.8691 (mptt) REVERT: F 782 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8539 (tm) REVERT: F 790 LEU cc_start: 0.8784 (pt) cc_final: 0.8188 (tm) REVERT: F 804 GLU cc_start: 0.8584 (tt0) cc_final: 0.7973 (tp30) REVERT: F 822 MET cc_start: 0.8307 (pmm) cc_final: 0.7852 (pp-130) REVERT: E 184 PHE cc_start: 0.8626 (p90) cc_final: 0.7805 (p90) REVERT: E 325 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6865 (t80) REVERT: E 346 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9121 (mt) REVERT: E 397 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7459 (t80) REVERT: E 420 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8562 (mt) REVERT: E 454 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: E 555 TRP cc_start: 0.7832 (m-10) cc_final: 0.7506 (m-10) REVERT: E 634 MET cc_start: -0.1500 (tpp) cc_final: -0.2516 (tmm) outliers start: 137 outliers final: 89 residues processed: 332 average time/residue: 0.5184 time to fit residues: 217.5524 Evaluate side-chains 342 residues out of total 3924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 218 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 822 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 183 TRP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 PHE Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 VAL Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 673 ILE Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 782 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 183 TRP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 344 GLU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 GLU Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain E residue 397 PHE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 585 ARG Chi-restraints excluded: chain E residue 725 VAL Chi-restraints excluded: chain E residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [354, 408, 412, 256, 304, 169, 144, 197, 49, 7, 277] chunk 354 optimal weight: 0.7980 chunk 408 optimal weight: 9.9990 chunk 412 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 304 optimal weight: 0.0970 chunk 169 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.136110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083724 restraints weight = 155085.933| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.34 r_work: 0.3080 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35160 Z= 0.114 Angle : 0.628 14.367 47622 Z= 0.303 Chirality : 0.042 0.207 5532 Planarity : 0.004 0.043 5892 Dihedral : 6.674 59.993 4580 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 3.44 % Allowed : 16.62 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 4182 helix: 0.36 (0.12), residues: 1881 sheet: -1.53 (0.22), residues: 617 loop : -0.08 (0.17), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 540 TYR 0.025 0.001 TYR D 369 PHE 0.027 0.001 PHE F 679 TRP 0.041 0.001 TRP F 555 HIS 0.005 0.000 HIS F 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (35148) covalent geometry : angle 0.62810 / 0.30 (47598) SS BOND : bond 0.00378 / 0.22 ( 12) SS BOND : angle 0.99581 / 0.74 ( 24) hydrogen bonds : bond 0.03566 / 2.34 ( 1442) hydrogen bonds : angle 4.03797 / 2.85 ( 3543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17508.08 seconds wall clock time: 297 minutes 31.85 seconds (17851.85 seconds total)