Starting phenix.real_space_refine on Sat Jul 4 15:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.map" model { file = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i91_35254/07_2026/8i91_35254.cif" } resolution = 3.3 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= 0.007 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 130 5.16 5 Cl 2 4.86 5 C 14100 2.51 5 N 3486 2.21 5 O 4044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21764 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "B" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} Chain: "C" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "D" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4552 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 557} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.86, per 1000 atoms: 0.22 Number of scatterers: 21764 At special positions: 0 Unit cell: (122.831, 138.049, 179.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 130 16.00 O 4044 8.00 N 3486 7.00 C 14100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B 703 " - " ASN B 131 " " NAG C 901 " - " ASN C 322 " " NAG D 703 " - " ASN D 131 " " NAG E 1 " - " ASN A 53 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN A 103 " " NAG H 1 " - " ASN A 432 " " NAG I 1 " - " ASN A 546 " " NAG J 1 " - " ASN A 690 " " NAG K 1 " - " ASN B 357 " " NAG L 1 " - " ASN C 53 " " NAG M 1 " - " ASN C 90 " " NAG N 1 " - " ASN C 103 " " NAG O 1 " - " ASN C 432 " " NAG P 1 " - " ASN C 546 " " NAG Q 1 " - " ASN C 690 " " NAG R 1 " - " ASN D 357 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 65.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.593A pdb=" N ASP A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.591A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.751A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.908A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.614A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.528A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.729A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.630A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.816A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.988A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.313A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.520A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.517A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.565A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.640A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.622A pdb=" N LEU B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 85 through 116 removed outlier: 4.203A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 168 through 185 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 272 through 320 removed outlier: 4.193A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.629A pdb=" N GLY B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.594A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.921A pdb=" N LEU B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.597A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 3.850A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.684A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.992A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.566A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.535A pdb=" N MET C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.592A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Proline residue: C 178 - end of helix removed outlier: 3.751A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.907A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.615A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.528A pdb=" N GLY C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.030A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.699A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 removed outlier: 3.606A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.728A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.630A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.817A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.648A pdb=" N ASN C 508 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 509 " --> pdb=" O VAL C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 509' Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.988A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.593A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 4.312A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.521A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.818A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.612A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.518A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.566A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 3.513A pdb=" N VAL C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE C 761 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.971A pdb=" N VAL D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.203A pdb=" N VAL D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.639A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.621A pdb=" N LEU D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.688A pdb=" N LEU D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.635A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 85 through 116 removed outlier: 4.202A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.613A pdb=" N LYS D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 192 through 202 removed outlier: 4.118A pdb=" N ALA D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.664A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 272 through 320 removed outlier: 4.192A pdb=" N ILE D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.622A pdb=" N GLU D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.628A pdb=" N SER D 349 " --> pdb=" O PRO D 345 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.680A pdb=" N GLU D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 416 removed outlier: 3.663A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.525A pdb=" N SER D 426 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 427' Processing helix chain 'D' and resid 431 through 445 removed outlier: 3.630A pdb=" N GLY D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.885A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 483 removed outlier: 3.828A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 482 " --> pdb=" O ILE D 478 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 491 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.356A pdb=" N ASP D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 3.595A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.920A pdb=" N LEU D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.923A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.726A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 removed outlier: 6.731A pdb=" N ASP A 693 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'B' and resid 535 through 538 Processing sheet with id=AA7, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.924A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.727A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 670 through 673 removed outlier: 6.731A pdb=" N ASP C 693 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB3, first strand: chain 'D' and resid 535 through 538 1045 hydrogen bonds defined for protein. 3045 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: 4.09 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6807 1.35 - 1.48: 6383 1.48 - 1.62: 8932 1.62 - 1.75: 0 1.75 - 1.88: 216 Bond restraints: 22338 Sorted by residual: bond pdb=" CA THR B 192 " pdb=" C THR B 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" CA THR D 192 " pdb=" C THR D 192 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" N PRO C 677 " pdb=" CD PRO C 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO A 677 " pdb=" CD PRO A 677 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N THR B 192 " pdb=" CA THR B 192 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.29e-02 6.01e+03 1.80e+01 ... (remaining 22333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 29581 2.70 - 5.40: 709 5.40 - 8.10: 80 8.10 - 10.80: 4 10.80 - 13.50: 8 Bond angle restraints: 30382 Sorted by residual: angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" N GLY D 193 " pdb=" CA GLY D 193 " pdb=" C GLY D 193 " ideal model delta sigma weight residual 112.64 118.43 -5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" C VAL D 45 " pdb=" N PRO D 46 " pdb=" CA PRO D 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C VAL B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta sigma weight residual 119.05 113.78 5.27 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C PHE D 228 " pdb=" N THR D 229 " pdb=" CA THR D 229 " ideal model delta sigma weight residual 120.49 113.77 6.72 1.42e+00 4.96e-01 2.24e+01 ... (remaining 30377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11041 17.75 - 35.50: 1303 35.50 - 53.25: 372 53.25 - 71.00: 92 71.00 - 88.75: 38 Dihedral angle restraints: 12846 sinusoidal: 5068 harmonic: 7778 Sorted by residual: dihedral pdb=" CA ALA D 500 " pdb=" C ALA D 500 " pdb=" N VAL D 501 " pdb=" CA VAL D 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA B 500 " pdb=" C ALA B 500 " pdb=" N VAL B 501 " pdb=" CA VAL B 501 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 46.42 46.58 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 12843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 3396 0.186 - 0.373: 24 0.373 - 0.559: 0 0.559 - 0.746: 0 0.746 - 0.932: 2 Chirality restraints: 3422 Sorted by residual: chirality pdb=" C1 NAG D 703 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D 703 " pdb=" O5 NAG D 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 131 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA TYR D 463 " pdb=" N TYR D 463 " pdb=" C TYR D 463 " pdb=" CB TYR D 463 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3419 not shown) Planarity restraints: 3808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 131 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN B 131 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 131 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN B 131 " -0.081 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 131 " -0.022 2.00e-02 2.50e+03 4.56e-02 2.59e+01 pdb=" CG ASN D 131 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 131 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN D 131 " 0.081 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 732 " -0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO A 733 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.051 5.00e-02 4.00e+02 ... (remaining 3805 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 144 2.45 - 3.06: 16119 3.06 - 3.67: 30575 3.67 - 4.29: 45658 4.29 - 4.90: 76502 Nonbonded interactions: 168998 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.837 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.837 2.230 nonbonded pdb=" O TYR B 265 " pdb=" O ASN B 266 " model vdw 1.948 3.040 nonbonded pdb=" O TYR D 265 " pdb=" O ASN D 266 " model vdw 1.948 3.040 nonbonded pdb=" O GLY D 485 " pdb=" N ARG D 487 " model vdw 2.027 3.120 ... (remaining 168993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.690 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5209 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 : 0.011 0.308 22384 Z= 0.515 Angle : 1.122 50.722 30498 Z= 0.619 Chirality : 0.062 0.932 3422 Planarity : 0.005 0.096 3790 Dihedral : 17.534 88.753 7824 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 2.15 % Allowed : 12.88 % Favored : 84.97 % Rotamer: Outliers : 8.31 % Allowed : 15.93 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.13), residues: 2648 helix: -2.56 (0.10), residues: 1562 sheet: -2.13 (0.57), residues: 68 loop : -3.64 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 582 TYR 0.022 0.002 TYR C 183 PHE 0.014 0.002 PHE A 274 TRP 0.030 0.002 TRP D 509 HIS 0.007 0.002 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.50 (22338) covalent geometry : angle 1.02707 / 0.60 (30382) SS BOND : bond 0.00850 / 0.55 ( 10) SS BOND : angle 3.34300 / 1.98 ( 20) hydrogen bonds : bond 0.18524 / 12.27 ( 1037) hydrogen bonds : angle 7.54924 / 5.32 ( 3045) metal coordination : bond 0.24273 / 11.20 ( 4) link_BETA1-4 : bond 0.00645 / 0.38 ( 14) link_BETA1-4 : angle 2.34888 / 1.34 ( 42) link_NAG-ASN : bond 0.01452 / 1.07 ( 18) link_NAG-ASN : angle 10.41391 / 6.60 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 556 time to evaluate : 0.617 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: A 86 GLN cc_start: 0.8063 (mp10) cc_final: 0.7743 (pm20) REVERT: A 154 ASN cc_start: 0.7847 (m110) cc_final: 0.7589 (m-40) REVERT: A 190 MET cc_start: 0.7952 (tmt) cc_final: 0.7605 (tmm) REVERT: A 199 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 210 ASN cc_start: 0.8639 (m-40) cc_final: 0.8189 (m-40) REVERT: A 276 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 309 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7829 (mmtp) REVERT: A 330 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 350 ASP cc_start: 0.5858 (t0) cc_final: 0.5540 (t70) REVERT: A 470 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7481 (ttmt) REVERT: A 559 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7444 (ptm-80) REVERT: A 568 LEU cc_start: 0.8230 (tp) cc_final: 0.7968 (tt) REVERT: A 572 ASN cc_start: 0.8587 (m-40) cc_final: 0.8246 (m-40) REVERT: A 577 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: A 601 ASN cc_start: 0.7091 (m-40) cc_final: 0.6873 (p0) REVERT: A 640 MET cc_start: 0.7358 (mmm) cc_final: 0.7114 (mmm) REVERT: A 651 MET cc_start: 0.7745 (mmm) cc_final: 0.7482 (mmm) REVERT: A 662 MET cc_start: 0.6406 (tpt) cc_final: 0.5962 (tpp) REVERT: A 760 LEU cc_start: 0.2040 (OUTLIER) cc_final: 0.1807 (tt) REVERT: B 101 TYR cc_start: 0.7121 (p90) cc_final: 0.6562 (p90) REVERT: B 136 ASP cc_start: 0.6947 (t0) cc_final: 0.6457 (p0) REVERT: B 324 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5552 (pm20) REVERT: B 333 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2851 (tp) REVERT: B 359 SER cc_start: 0.7524 (t) cc_final: 0.7182 (p) REVERT: B 380 GLU cc_start: 0.4954 (mm-30) cc_final: 0.4056 (mm-30) REVERT: B 406 SER cc_start: 0.6705 (OUTLIER) cc_final: 0.6489 (p) REVERT: B 473 VAL cc_start: 0.7218 (t) cc_final: 0.6935 (t) REVERT: C 38 ASP cc_start: 0.8521 (m-30) cc_final: 0.8270 (m-30) REVERT: C 113 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6772 (p) REVERT: C 156 LEU cc_start: 0.8465 (mt) cc_final: 0.8192 (tp) REVERT: C 182 GLU cc_start: 0.5355 (tt0) cc_final: 0.5081 (mt-10) REVERT: C 330 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7529 (p0) REVERT: C 366 MET cc_start: 0.8051 (ttt) cc_final: 0.7822 (ttm) REVERT: C 383 MET cc_start: 0.8245 (mtp) cc_final: 0.8024 (mtt) REVERT: C 408 MET cc_start: 0.8599 (mpp) cc_final: 0.8320 (mmm) REVERT: C 416 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8338 (ttpt) REVERT: C 625 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7708 (mttt) REVERT: C 637 ASP cc_start: 0.7164 (m-30) cc_final: 0.6866 (m-30) REVERT: C 667 GLU cc_start: 0.5884 (pp20) cc_final: 0.5173 (mp0) REVERT: C 668 GLU cc_start: 0.7702 (pm20) cc_final: 0.7367 (pm20) REVERT: C 669 ASP cc_start: 0.6895 (m-30) cc_final: 0.6671 (m-30) REVERT: C 740 SER cc_start: 0.1268 (OUTLIER) cc_final: 0.1061 (m) REVERT: D 187 ARG cc_start: 0.3551 (OUTLIER) cc_final: 0.3339 (mtt180) REVERT: D 260 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5757 (tt) REVERT: D 281 LEU cc_start: 0.7763 (mt) cc_final: 0.7521 (tp) REVERT: D 324 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5664 (mm-30) REVERT: D 334 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: D 344 TYR cc_start: 0.7544 (m-80) cc_final: 0.6778 (m-80) outliers start: 192 outliers final: 38 residues processed: 707 average time/residue: 0.1427 time to fit residues: 157.1028 Evaluate side-chains 392 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 149 ASN A 250 ASN A 345 HIS A 493 HIS A 505 HIS A 556 ASN A 586 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 736 GLN B 118 GLN B 275 HIS B 283 ASN B 410 ASN B 537 GLN C 33 ASN C 42 GLN C 63 ASN C 149 ASN C 154 ASN C 239 HIS C 250 ASN C 345 HIS C 493 HIS C 505 HIS C 556 ASN C 586 ASN C 599 ASN C 682 ASN C 736 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 283 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.246038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.225249 restraints weight = 26350.747| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 1.08 r_work: 0.4289 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4258 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22384 Z= 0.178 Angle : 0.775 11.297 30498 Z= 0.387 Chirality : 0.048 0.309 3422 Planarity : 0.005 0.099 3790 Dihedral : 8.533 88.001 2969 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 4.24 % Allowed : 19.31 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2648 helix: -0.70 (0.13), residues: 1584 sheet: -1.65 (0.55), residues: 82 loop : -2.94 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 169 TYR 0.029 0.002 TYR B 210 PHE 0.026 0.002 PHE A 746 TRP 0.022 0.001 TRP B 509 HIS 0.009 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (22338) covalent geometry : angle 0.76216 / 0.38 (30382) SS BOND : bond 0.02395 / 1.41 ( 10) SS BOND : angle 2.61286 / 1.60 ( 20) hydrogen bonds : bond 0.06014 / 3.88 ( 1037) hydrogen bonds : angle 4.88968 / 3.40 ( 3045) metal coordination : bond 0.01064 / 0.50 ( 4) link_BETA1-4 : bond 0.00574 / 0.28 ( 14) link_BETA1-4 : angle 1.74019 / 0.96 ( 42) link_NAG-ASN : bond 0.00761 / 0.56 ( 18) link_NAG-ASN : angle 2.67477 / 1.83 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 363 time to evaluate : 0.683 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: A 154 ASN cc_start: 0.8151 (m110) cc_final: 0.7903 (m-40) REVERT: A 228 HIS cc_start: 0.7440 (t70) cc_final: 0.7101 (m170) REVERT: A 276 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 768 ARG cc_start: -0.0577 (OUTLIER) cc_final: -0.2403 (mmp-170) REVERT: B 101 TYR cc_start: 0.6734 (p90) cc_final: 0.6401 (p90) REVERT: C 662 MET cc_start: 0.7841 (tpp) cc_final: 0.7484 (tpt) REVERT: C 740 SER cc_start: 0.3481 (OUTLIER) cc_final: 0.3106 (m) REVERT: D 69 MET cc_start: 0.5933 (mmt) cc_final: 0.5586 (mmt) REVERT: D 149 TRP cc_start: 0.5692 (t60) cc_final: 0.5362 (t-100) REVERT: D 398 MET cc_start: 0.6511 (tmm) cc_final: 0.6237 (tmm) outliers start: 98 outliers final: 36 residues processed: 442 average time/residue: 0.1241 time to fit residues: 89.7328 Evaluate side-chains 316 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 256 optimal weight: 30.0000 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 340 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN C 535 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.241165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215211 restraints weight = 26272.368| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 1.39 r_work: 0.4112 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22384 Z= 0.155 Angle : 0.691 11.155 30498 Z= 0.341 Chirality : 0.045 0.301 3422 Planarity : 0.005 0.086 3790 Dihedral : 6.479 59.972 2905 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.36 % Favored : 92.41 % Rotamer: Outliers : 3.46 % Allowed : 19.70 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.16), residues: 2648 helix: -0.06 (0.13), residues: 1596 sheet: -1.55 (0.57), residues: 70 loop : -2.42 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.021 0.001 TYR C 83 PHE 0.025 0.002 PHE B 110 TRP 0.040 0.002 TRP D 168 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22338) covalent geometry : angle 0.67450 / 0.34 (30382) SS BOND : bond 0.00845 / 0.50 ( 10) SS BOND : angle 1.87101 / 1.13 ( 20) hydrogen bonds : bond 0.05199 / 3.39 ( 1037) hydrogen bonds : angle 4.48842 / 3.11 ( 3045) metal coordination : bond 0.00398 / 0.19 ( 4) link_BETA1-4 : bond 0.00382 / 0.22 ( 14) link_BETA1-4 : angle 1.78088 / 1.01 ( 42) link_NAG-ASN : bond 0.00828 / 0.63 ( 18) link_NAG-ASN : angle 3.11676 / 2.10 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 0.797 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: A 154 ASN cc_start: 0.8277 (m110) cc_final: 0.8054 (m110) REVERT: A 228 HIS cc_start: 0.7658 (t70) cc_final: 0.7347 (m170) REVERT: A 340 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6994 (tp40) REVERT: A 356 PHE cc_start: 0.8078 (m-80) cc_final: 0.7839 (m-80) REVERT: A 479 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 768 ARG cc_start: -0.0842 (OUTLIER) cc_final: -0.4047 (mpp80) REVERT: B 101 TYR cc_start: 0.6899 (p90) cc_final: 0.6570 (p90) REVERT: C 401 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7428 (t-90) REVERT: C 662 MET cc_start: 0.7986 (tpp) cc_final: 0.7688 (tpt) REVERT: D 205 CYS cc_start: 0.5132 (OUTLIER) cc_final: 0.4555 (m) outliers start: 80 outliers final: 48 residues processed: 349 average time/residue: 0.1152 time to fit residues: 66.8046 Evaluate side-chains 296 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 249 optimal weight: 10.0000 chunk 80 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 231 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 535 HIS D 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.242984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.221243 restraints weight = 26067.873| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.16 r_work: 0.4253 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4222 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22384 Z= 0.135 Angle : 0.642 11.525 30498 Z= 0.317 Chirality : 0.043 0.283 3422 Planarity : 0.004 0.073 3790 Dihedral : 6.084 59.603 2899 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.34 % Favored : 93.43 % Rotamer: Outliers : 3.29 % Allowed : 20.13 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2648 helix: 0.22 (0.13), residues: 1608 sheet: -1.50 (0.56), residues: 70 loop : -2.36 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.020 0.001 TYR B 339 PHE 0.028 0.002 PHE D 457 TRP 0.023 0.001 TRP D 149 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22338) covalent geometry : angle 0.62820 / 0.31 (30382) SS BOND : bond 0.00794 / 0.50 ( 10) SS BOND : angle 1.73257 / 1.04 ( 20) hydrogen bonds : bond 0.04648 / 3.01 ( 1037) hydrogen bonds : angle 4.28356 / 2.97 ( 3045) metal coordination : bond 0.00223 / 0.10 ( 4) link_BETA1-4 : bond 0.00432 / 0.21 ( 14) link_BETA1-4 : angle 1.71675 / 0.95 ( 42) link_NAG-ASN : bond 0.00822 / 0.62 ( 18) link_NAG-ASN : angle 2.74620 / 1.80 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 266 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8428 (m110) cc_final: 0.8200 (m110) REVERT: A 228 HIS cc_start: 0.7620 (t70) cc_final: 0.7401 (m170) REVERT: A 360 MET cc_start: 0.7171 (ttp) cc_final: 0.6953 (ttp) REVERT: A 479 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 768 ARG cc_start: -0.0757 (OUTLIER) cc_final: -0.3820 (mpp80) REVERT: B 101 TYR cc_start: 0.6765 (p90) cc_final: 0.6514 (p90) REVERT: C 401 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: C 480 MET cc_start: 0.9052 (mtp) cc_final: 0.8768 (mtm) REVERT: C 662 MET cc_start: 0.7841 (tpp) cc_final: 0.7557 (tpt) REVERT: D 205 CYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4710 (m) REVERT: D 351 MET cc_start: 0.6116 (mtp) cc_final: 0.5415 (ttm) outliers start: 76 outliers final: 49 residues processed: 319 average time/residue: 0.1198 time to fit residues: 62.8919 Evaluate side-chains 293 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 152 optimal weight: 0.8980 chunk 245 optimal weight: 30.0000 chunk 153 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.239249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.212657 restraints weight = 25974.574| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 1.43 r_work: 0.3788 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22384 Z= 0.137 Angle : 0.641 12.207 30498 Z= 0.314 Chirality : 0.043 0.298 3422 Planarity : 0.004 0.063 3790 Dihedral : 5.744 59.537 2893 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.53 % Favored : 93.24 % Rotamer: Outliers : 3.29 % Allowed : 20.69 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.91 (0.17), residues: 2648 helix: 0.37 (0.13), residues: 1640 sheet: -1.46 (0.56), residues: 70 loop : -2.27 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 70 TYR 0.019 0.001 TYR B 554 PHE 0.030 0.002 PHE D 110 TRP 0.026 0.001 TRP D 149 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22338) covalent geometry : angle 0.62514 / 0.31 (30382) SS BOND : bond 0.00673 / 0.41 ( 10) SS BOND : angle 1.80973 / 1.10 ( 20) hydrogen bonds : bond 0.04471 / 2.91 ( 1037) hydrogen bonds : angle 4.14533 / 2.88 ( 3045) metal coordination : bond 0.00246 / 0.11 ( 4) link_BETA1-4 : bond 0.00365 / 0.20 ( 14) link_BETA1-4 : angle 1.71555 / 0.97 ( 42) link_NAG-ASN : bond 0.00777 / 0.60 ( 18) link_NAG-ASN : angle 2.94357 / 1.91 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 254 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 742 TRP cc_start: 0.7115 (OUTLIER) cc_final: 0.5789 (p90) REVERT: A 757 ILE cc_start: 0.2028 (OUTLIER) cc_final: 0.1696 (tp) REVERT: A 768 ARG cc_start: -0.1498 (OUTLIER) cc_final: -0.4005 (mpp80) REVERT: B 225 MET cc_start: 0.7306 (tpp) cc_final: 0.6616 (ptm) REVERT: B 446 MET cc_start: 0.6751 (mmm) cc_final: 0.6507 (mmm) REVERT: B 496 MET cc_start: 0.3452 (mmm) cc_final: 0.2997 (mpp) REVERT: C 401 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.7954 (t-90) REVERT: C 480 MET cc_start: 0.9077 (mtp) cc_final: 0.8837 (mtm) REVERT: C 662 MET cc_start: 0.7824 (tpp) cc_final: 0.7586 (tpt) REVERT: C 667 GLU cc_start: 0.7039 (mp0) cc_final: 0.6615 (mp0) REVERT: D 69 MET cc_start: 0.5500 (mmt) cc_final: 0.5076 (mmt) REVERT: D 139 CYS cc_start: 0.4306 (OUTLIER) cc_final: 0.3802 (t) outliers start: 76 outliers final: 49 residues processed: 310 average time/residue: 0.1268 time to fit residues: 64.8597 Evaluate side-chains 283 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 102 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 3 optimal weight: 0.0570 chunk 258 optimal weight: 8.9990 chunk 231 optimal weight: 30.0000 overall best weight: 2.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN C 24 GLN D 106 ASN D 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.231649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.188142 restraints weight = 25641.381| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.41 r_work: 0.3581 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22384 Z= 0.264 Angle : 0.752 12.261 30498 Z= 0.373 Chirality : 0.048 0.331 3422 Planarity : 0.005 0.053 3790 Dihedral : 5.960 58.145 2893 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.65 % Favored : 93.13 % Rotamer: Outliers : 3.64 % Allowed : 21.47 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2648 helix: 0.13 (0.13), residues: 1632 sheet: -0.39 (0.71), residues: 50 loop : -2.39 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.030 0.002 TYR A 183 PHE 0.025 0.002 PHE A 314 TRP 0.029 0.002 TRP D 149 HIS 0.012 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.26 (22338) covalent geometry : angle 0.73633 / 0.37 (30382) SS BOND : bond 0.01669 / 1.08 ( 10) SS BOND : angle 2.47243 / 1.57 ( 20) hydrogen bonds : bond 0.05668 / 3.68 ( 1037) hydrogen bonds : angle 4.35720 / 3.05 ( 3045) metal coordination : bond 0.00777 / 0.34 ( 4) link_BETA1-4 : bond 0.00543 / 0.24 ( 14) link_BETA1-4 : angle 1.95061 / 1.03 ( 42) link_NAG-ASN : bond 0.00778 / 0.60 ( 18) link_NAG-ASN : angle 2.99668 / 1.91 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 260 time to evaluate : 0.762 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: A 206 ASP cc_start: 0.8429 (t0) cc_final: 0.8200 (t0) REVERT: A 416 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8393 (tptp) REVERT: A 479 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 509 ASP cc_start: 0.7792 (t0) cc_final: 0.7498 (t70) REVERT: A 768 ARG cc_start: -0.1548 (OUTLIER) cc_final: -0.3945 (mpp80) REVERT: B 27 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.5537 (m110) REVERT: B 496 MET cc_start: 0.2958 (mmm) cc_final: 0.2540 (mpp) REVERT: C 114 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7872 (ptmm) REVERT: C 269 ASP cc_start: 0.7429 (t0) cc_final: 0.7053 (t70) REVERT: C 480 MET cc_start: 0.9029 (mtp) cc_final: 0.8817 (mtm) REVERT: C 556 ASN cc_start: 0.8622 (t0) cc_final: 0.8334 (t0) REVERT: C 662 MET cc_start: 0.8264 (tpp) cc_final: 0.8053 (tmm) REVERT: C 667 GLU cc_start: 0.7208 (mp0) cc_final: 0.6850 (mp0) REVERT: D 69 MET cc_start: 0.5588 (mmt) cc_final: 0.5158 (mmt) REVERT: D 139 CYS cc_start: 0.5015 (OUTLIER) cc_final: 0.4568 (t) REVERT: D 149 TRP cc_start: 0.6438 (t60) cc_final: 0.6140 (t60) REVERT: D 205 CYS cc_start: 0.5524 (OUTLIER) cc_final: 0.4903 (m) REVERT: D 446 MET cc_start: 0.7537 (mmm) cc_final: 0.7282 (mmp) outliers start: 84 outliers final: 51 residues processed: 325 average time/residue: 0.1234 time to fit residues: 65.7917 Evaluate side-chains 288 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN D 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.234130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189532 restraints weight = 25723.176| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.43 r_work: 0.3569 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22384 Z= 0.136 Angle : 0.643 11.809 30498 Z= 0.316 Chirality : 0.043 0.320 3422 Planarity : 0.004 0.049 3790 Dihedral : 5.694 59.246 2893 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.62 % Rotamer: Outliers : 2.68 % Allowed : 21.99 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.79 (0.16), residues: 2648 helix: 0.44 (0.13), residues: 1634 sheet: -1.25 (0.57), residues: 70 loop : -2.18 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.026 0.001 TYR B 33 PHE 0.018 0.001 PHE D 228 TRP 0.021 0.001 TRP D 149 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22338) covalent geometry : angle 0.62797 / 0.31 (30382) SS BOND : bond 0.00869 / 0.52 ( 10) SS BOND : angle 2.05538 / 1.31 ( 20) hydrogen bonds : bond 0.04495 / 2.93 ( 1037) hydrogen bonds : angle 4.17070 / 2.92 ( 3045) metal coordination : bond 0.00320 / 0.14 ( 4) link_BETA1-4 : bond 0.00381 / 0.24 ( 14) link_BETA1-4 : angle 1.66078 / 0.95 ( 42) link_NAG-ASN : bond 0.00766 / 0.58 ( 18) link_NAG-ASN : angle 2.85861 / 1.84 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8168 (tt0) cc_final: 0.7891 (tt0) REVERT: A 416 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8432 (tptp) REVERT: A 479 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 768 ARG cc_start: -0.1550 (OUTLIER) cc_final: -0.3894 (mpp80) REVERT: B 496 MET cc_start: 0.3409 (mmm) cc_final: 0.2958 (mpp) REVERT: C 401 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8635 (t-90) REVERT: C 480 MET cc_start: 0.9011 (mtp) cc_final: 0.8782 (mtm) REVERT: D 37 MET cc_start: 0.7891 (ppp) cc_final: 0.7554 (ppp) REVERT: D 69 MET cc_start: 0.5607 (mmt) cc_final: 0.5200 (mmt) REVERT: D 139 CYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4426 (t) REVERT: D 205 CYS cc_start: 0.5535 (OUTLIER) cc_final: 0.4949 (m) REVERT: D 351 MET cc_start: 0.7398 (mtp) cc_final: 0.6171 (ttm) REVERT: D 446 MET cc_start: 0.7584 (mmm) cc_final: 0.7371 (mmp) outliers start: 62 outliers final: 43 residues processed: 302 average time/residue: 0.1304 time to fit residues: 64.9799 Evaluate side-chains 283 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 225 optimal weight: 0.9990 chunk 253 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS D 234 GLN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.234423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191400 restraints weight = 25647.309| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.38 r_work: 0.3612 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22384 Z= 0.132 Angle : 0.648 11.699 30498 Z= 0.317 Chirality : 0.043 0.332 3422 Planarity : 0.004 0.047 3790 Dihedral : 5.511 58.733 2893 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.19 % Favored : 93.62 % Rotamer: Outliers : 2.77 % Allowed : 22.29 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.68 (0.17), residues: 2648 helix: 0.50 (0.13), residues: 1650 sheet: -1.22 (0.57), residues: 70 loop : -2.12 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.033 0.001 TYR A 50 PHE 0.020 0.001 PHE D 228 TRP 0.019 0.001 TRP D 149 HIS 0.009 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22338) covalent geometry : angle 0.63446 / 0.31 (30382) SS BOND : bond 0.00790 / 0.49 ( 10) SS BOND : angle 1.63333 / 0.95 ( 20) hydrogen bonds : bond 0.04379 / 2.84 ( 1037) hydrogen bonds : angle 4.12746 / 2.89 ( 3045) metal coordination : bond 0.00140 / 0.06 ( 4) link_BETA1-4 : bond 0.00424 / 0.24 ( 14) link_BETA1-4 : angle 1.62785 / 0.90 ( 42) link_NAG-ASN : bond 0.00705 / 0.55 ( 18) link_NAG-ASN : angle 2.75239 / 1.78 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8867 (mmt) cc_final: 0.7599 (mmt) REVERT: A 208 GLU cc_start: 0.8168 (tt0) cc_final: 0.7923 (tt0) REVERT: A 416 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8534 (tptp) REVERT: A 479 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8506 (mt-10) REVERT: A 722 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9035 (tp) REVERT: A 768 ARG cc_start: -0.1635 (OUTLIER) cc_final: -0.3904 (mpp80) REVERT: B 27 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.5699 (m110) REVERT: B 225 MET cc_start: 0.7722 (tpp) cc_final: 0.6589 (ptm) REVERT: B 262 PHE cc_start: 0.6267 (m-10) cc_final: 0.6066 (m-80) REVERT: C 401 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8723 (t-90) REVERT: C 480 MET cc_start: 0.9068 (mtp) cc_final: 0.8842 (mtm) REVERT: C 667 GLU cc_start: 0.7850 (mp0) cc_final: 0.7633 (mp0) REVERT: D 37 MET cc_start: 0.7857 (ppp) cc_final: 0.7606 (ppp) REVERT: D 69 MET cc_start: 0.5582 (mmt) cc_final: 0.5205 (mmt) REVERT: D 139 CYS cc_start: 0.5073 (OUTLIER) cc_final: 0.4631 (t) REVERT: D 351 MET cc_start: 0.7464 (mtp) cc_final: 0.6298 (ttm) outliers start: 64 outliers final: 46 residues processed: 299 average time/residue: 0.1184 time to fit residues: 58.4407 Evaluate side-chains 282 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 183 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 255 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** D 270 ASN ** 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 = 0.4503 r_free = 0.4503 target = 0.230741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.202799 restraints weight = 25361.367| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.40 r_work: 0.3493 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22384 Z= 0.233 Angle : 0.714 12.276 30498 Z= 0.353 Chirality : 0.046 0.339 3422 Planarity : 0.005 0.050 3790 Dihedral : 5.593 59.100 2893 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.24 % Rotamer: Outliers : 2.55 % Allowed : 22.99 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2648 helix: 0.36 (0.13), residues: 1656 sheet: -1.73 (0.69), residues: 54 loop : -2.19 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 219 TYR 0.027 0.002 TYR B 33 PHE 0.023 0.002 PHE B 114 TRP 0.025 0.002 TRP D 241 HIS 0.024 0.002 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (22338) covalent geometry : angle 0.70102 / 0.35 (30382) SS BOND : bond 0.00804 / 0.49 ( 10) SS BOND : angle 2.23911 / 1.39 ( 20) hydrogen bonds : bond 0.05090 / 3.29 ( 1037) hydrogen bonds : angle 4.23980 / 2.97 ( 3045) metal coordination : bond 0.00371 / 0.16 ( 4) link_BETA1-4 : bond 0.00345 / 0.21 ( 14) link_BETA1-4 : angle 1.62829 / 0.91 ( 42) link_NAG-ASN : bond 0.00709 / 0.55 ( 18) link_NAG-ASN : angle 2.80951 / 1.80 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8564 (tt0) cc_final: 0.8363 (tt0) REVERT: A 416 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8422 (tptp) REVERT: A 479 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8620 (mt-10) REVERT: A 509 ASP cc_start: 0.8352 (t0) cc_final: 0.8060 (t70) REVERT: A 722 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9139 (tp) REVERT: B 262 PHE cc_start: 0.6291 (m-10) cc_final: 0.5966 (m-80) REVERT: B 508 MET cc_start: 0.4659 (mtm) cc_final: 0.3748 (ttm) REVERT: C 269 ASP cc_start: 0.8354 (t0) cc_final: 0.8112 (t70) REVERT: C 401 HIS cc_start: 0.9286 (OUTLIER) cc_final: 0.8749 (t-90) REVERT: C 480 MET cc_start: 0.9161 (mtp) cc_final: 0.8955 (mtm) REVERT: C 667 GLU cc_start: 0.7739 (mp0) cc_final: 0.7534 (mp0) REVERT: C 668 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: D 37 MET cc_start: 0.7960 (ppp) cc_final: 0.7675 (ppp) REVERT: D 69 MET cc_start: 0.4929 (mmt) cc_final: 0.4662 (mmt) REVERT: D 139 CYS cc_start: 0.5156 (OUTLIER) cc_final: 0.4594 (t) REVERT: D 149 TRP cc_start: 0.6656 (t60) cc_final: 0.5753 (t-100) REVERT: D 205 CYS cc_start: 0.5457 (OUTLIER) cc_final: 0.4879 (m) outliers start: 59 outliers final: 46 residues processed: 296 average time/residue: 0.1198 time to fit residues: 58.5224 Evaluate side-chains 291 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 14 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 190 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 599 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.233039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197951 restraints weight = 24995.722| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.74 r_work: 0.3769 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22384 Z= 0.135 Angle : 0.645 11.105 30498 Z= 0.317 Chirality : 0.043 0.341 3422 Planarity : 0.004 0.045 3790 Dihedral : 5.288 58.547 2889 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.16 % Allowed : 23.16 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.60 (0.17), residues: 2648 helix: 0.55 (0.13), residues: 1666 sheet: -1.68 (0.69), residues: 54 loop : -2.06 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.025 0.001 TYR B 33 PHE 0.035 0.001 PHE D 117 TRP 0.018 0.001 TRP D 149 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22338) covalent geometry : angle 0.63214 / 0.31 (30382) SS BOND : bond 0.00680 / 0.41 ( 10) SS BOND : angle 1.69702 / 1.04 ( 20) hydrogen bonds : bond 0.04324 / 2.80 ( 1037) hydrogen bonds : angle 4.14864 / 2.91 ( 3045) metal coordination : bond 0.00123 / 0.06 ( 4) link_BETA1-4 : bond 0.00409 / 0.25 ( 14) link_BETA1-4 : angle 1.53320 / 0.88 ( 42) link_NAG-ASN : bond 0.00688 / 0.53 ( 18) link_NAG-ASN : angle 2.70985 / 1.75 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.808 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: A 208 GLU cc_start: 0.8042 (tt0) cc_final: 0.7766 (tt0) REVERT: A 479 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 722 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8971 (tp) REVERT: B 225 MET cc_start: 0.7333 (tpp) cc_final: 0.6797 (ptm) REVERT: B 407 MET cc_start: 0.6156 (tpt) cc_final: 0.5936 (tpp) REVERT: C 269 ASP cc_start: 0.7722 (t0) cc_final: 0.7367 (t70) REVERT: C 401 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8631 (t-90) REVERT: C 480 MET cc_start: 0.9005 (mtp) cc_final: 0.8787 (mtm) REVERT: C 667 GLU cc_start: 0.7237 (mp0) cc_final: 0.7031 (mp0) REVERT: C 668 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: D 69 MET cc_start: 0.5497 (mmt) cc_final: 0.5097 (mmt) REVERT: D 139 CYS cc_start: 0.4894 (OUTLIER) cc_final: 0.4405 (t) REVERT: D 149 TRP cc_start: 0.6386 (t60) cc_final: 0.6002 (t-100) outliers start: 50 outliers final: 43 residues processed: 285 average time/residue: 0.1250 time to fit residues: 58.7044 Evaluate side-chains 279 residues out of total 2310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 184 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 61 optimal weight: 0.0060 chunk 255 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 251 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** D 270 ASN ** 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 = 0.4511 r_free = 0.4511 target = 0.232978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.199131 restraints weight = 25133.916| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.63 r_work: 0.3772 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22384 Z= 0.159 Angle : 0.669 13.121 30498 Z= 0.327 Chirality : 0.044 0.342 3422 Planarity : 0.004 0.046 3790 Dihedral : 5.260 58.246 2889 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 2.29 % Allowed : 23.72 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2648 helix: 0.58 (0.13), residues: 1646 sheet: -1.64 (0.69), residues: 54 loop : -2.04 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.026 0.001 TYR B 33 PHE 0.032 0.002 PHE D 117 TRP 0.018 0.001 TRP D 149 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22338) covalent geometry : angle 0.65189 / 0.32 (30382) SS BOND : bond 0.00851 / 0.51 ( 10) SS BOND : angle 3.53657 / 1.88 ( 20) hydrogen bonds : bond 0.04495 / 2.91 ( 1037) hydrogen bonds : angle 4.15239 / 2.91 ( 3045) metal coordination : bond 0.00190 / 0.08 ( 4) link_BETA1-4 : bond 0.00354 / 0.22 ( 14) link_BETA1-4 : angle 1.52788 / 0.87 ( 42) link_NAG-ASN : bond 0.00668 / 0.52 ( 18) link_NAG-ASN : angle 2.69545 / 1.73 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.19 seconds wall clock time: 81 minutes 40.48 seconds (4900.48 seconds total)