Starting phenix.real_space_refine on Sat Jul 4 17:06:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.map" model { file = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i92_35255/07_2026/8i92_35255.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 128 5.16 5 C 14476 2.51 5 N 3568 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 22344 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: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} 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: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.73, per 1000 atoms: 0.21 Number of scatterers: 22344 At special positions: 0 Unit cell: (109.787, 135.875, 183.703, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 128 16.00 O 4170 8.00 N 3568 7.00 C 14476 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=2.04 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 153 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 383 " 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 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " 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=2, 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 702 " - " ASN B 182 " " NAG B 703 " - " ASN B 158 " " NAG B 704 " - " ASN B 368 " " NAG B 705 " - " ASN B 354 " " NAG C 901 " - " ASN C 322 " " NAG D 702 " - " ASN D 182 " " NAG D 703 " - " ASN D 158 " " NAG D 704 " - " ASN D 368 " " NAG D 705 " - " ASN D 354 " " 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 258 " " 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 258 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 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 " 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 12 sheets defined 65.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.251A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.021A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.090A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.618A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.712A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.248A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.760A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.854A 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 208 removed outlier: 3.827A pdb=" N GLU A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 220 through 230 removed outlier: 4.064A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.534A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' 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 293 through 299 removed outlier: 3.969A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.088A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.915A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.855A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.478A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.602A 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: 3.641A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.578A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.755A 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 534 removed outlier: 3.900A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.731A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.820A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.577A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.752A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.619A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.644A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 removed outlier: 3.617A pdb=" N VAL A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 4.081A pdb=" N ILE A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.076A pdb=" N SER B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.588A pdb=" N CYS B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 removed outlier: 4.065A pdb=" N TYR B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 142 removed outlier: 3.959A pdb=" N GLY B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.887A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 3.691A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.935A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.204A pdb=" N THR B 256 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.830A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 299 through 349 Processing helix chain 'B' and resid 359 through 371 Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 446 removed outlier: 3.504A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.939A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.543A pdb=" N LEU B 475 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.659A pdb=" N TRP B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.489A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.575A pdb=" N GLN B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 554 removed outlier: 3.790A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.605A pdb=" N VAL B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 5.146A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 4.004A pdb=" N ALA B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.251A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 4.021A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 4.090A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 130 removed outlier: 3.618A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.711A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 193 removed outlier: 4.248A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.760A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.855A 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 208 removed outlier: 3.827A pdb=" N GLU C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 220 through 230 removed outlier: 4.064A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.534A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' 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 293 through 299 removed outlier: 3.968A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.697A pdb=" N GLU C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.088A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.915A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.854A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.478A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.601A 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: 3.640A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 505 through 509 removed outlier: 3.578A pdb=" N ASN C 508 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 3.755A 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 534 removed outlier: 3.900A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.731A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.820A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.577A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.752A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.619A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.644A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 642 " --> pdb=" O ASN C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 716 removed outlier: 3.618A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 4.081A pdb=" N ILE C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 31 removed outlier: 4.076A pdb=" N SER D 30 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.589A pdb=" N CYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 64 removed outlier: 4.066A pdb=" N TYR D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 142 removed outlier: 3.959A pdb=" N GLY D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.886A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.691A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.935A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.203A pdb=" N THR D 256 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.830A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 299 through 349 Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 412 through 446 removed outlier: 3.505A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.940A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.543A pdb=" N LEU D 475 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.658A pdb=" N TRP D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 4.488A pdb=" N ALA D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.575A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 554 removed outlier: 3.789A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 554 " --> pdb=" O PHE D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 591 removed outlier: 3.605A pdb=" N VAL D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 608 removed outlier: 5.145A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 4.004A pdb=" N ALA D 601 " --> pdb=" O ILE D 597 " (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: 5.906A 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: 3.701A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.676A 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: 6.434A 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 559 through 562 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: 5.906A 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: 3.700A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.676A 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: 6.434A 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 559 through 562 1091 hydrogen bonds defined for protein. 3189 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: 3.30 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6824 1.34 - 1.46: 6109 1.46 - 1.59: 9805 1.59 - 1.71: 0 1.71 - 1.84: 210 Bond restraints: 22948 Sorted by residual: bond pdb=" CA GLU A 467 " pdb=" C GLU A 467 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.72e-02 3.38e+03 1.13e+01 bond pdb=" CA GLU C 467 " pdb=" C GLU C 467 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.72e-02 3.38e+03 1.10e+01 bond pdb=" CA ALA A 193 " pdb=" C ALA A 193 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.80e-02 3.09e+03 9.73e+00 bond pdb=" CA ALA C 193 " pdb=" C ALA C 193 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.80e-02 3.09e+03 9.73e+00 bond pdb=" C SER C 611 " pdb=" N PRO C 612 " ideal model delta sigma weight residual 1.335 1.299 0.036 1.19e-02 7.06e+03 9.11e+00 ... (remaining 22943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 29365 1.83 - 3.67: 1639 3.67 - 5.50: 178 5.50 - 7.33: 48 7.33 - 9.16: 6 Bond angle restraints: 31236 Sorted by residual: angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 114.56 106.98 7.58 1.27e+00 6.20e-01 3.56e+01 angle pdb=" N GLU C 87 " pdb=" CA GLU C 87 " pdb=" C GLU C 87 " ideal model delta sigma weight residual 114.56 107.05 7.51 1.27e+00 6.20e-01 3.50e+01 angle pdb=" N GLU D 352 " pdb=" CA GLU D 352 " pdb=" C GLU D 352 " ideal model delta sigma weight residual 111.07 116.63 -5.56 1.07e+00 8.73e-01 2.70e+01 angle pdb=" N GLU B 352 " pdb=" CA GLU B 352 " pdb=" C GLU B 352 " ideal model delta sigma weight residual 111.07 116.60 -5.53 1.07e+00 8.73e-01 2.67e+01 angle pdb=" N VAL D 55 " pdb=" CA VAL D 55 " pdb=" C VAL D 55 " ideal model delta sigma weight residual 112.96 108.19 4.77 1.00e+00 1.00e+00 2.27e+01 ... (remaining 31231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11527 17.98 - 35.96: 1194 35.96 - 53.95: 322 53.95 - 71.93: 75 71.93 - 89.91: 32 Dihedral angle restraints: 13150 sinusoidal: 5240 harmonic: 7910 Sorted by residual: dihedral pdb=" CA THR C 730 " pdb=" C THR C 730 " pdb=" N LEU C 731 " pdb=" CA LEU C 731 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA THR A 730 " pdb=" C THR A 730 " pdb=" N LEU A 731 " pdb=" CA LEU A 731 " ideal model delta harmonic sigma weight residual -180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 383 " pdb=" CB CYS D 383 " ideal model delta sinusoidal sigma weight residual -86.00 -131.02 45.02 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 13147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2404 0.054 - 0.109: 960 0.109 - 0.163: 138 0.163 - 0.217: 19 0.217 - 0.272: 7 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA ILE C 727 " pdb=" N ILE C 727 " pdb=" C ILE C 727 " pdb=" CB ILE C 727 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A 727 " pdb=" N ILE A 727 " pdb=" C ILE A 727 " pdb=" CB ILE A 727 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3525 not shown) Planarity restraints: 3938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 676 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO C 677 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 677 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 677 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 676 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 677 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 687 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 688 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.028 5.00e-02 4.00e+02 ... (remaining 3935 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 107 2.45 - 3.07: 16162 3.07 - 3.68: 31668 3.68 - 4.29: 47942 4.29 - 4.90: 80606 Nonbonded interactions: 176485 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.843 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.843 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.009 2.230 nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.009 2.230 nonbonded pdb=" N ASP C 367 " pdb=" OD1 ASP C 367 " model vdw 2.155 3.120 ... (remaining 176480 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.910 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.013 0.302 23002 Z= 0.622 Angle : 0.953 9.163 31370 Z= 0.546 Chirality : 0.055 0.272 3528 Planarity : 0.005 0.087 3914 Dihedral : 16.576 89.908 8032 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.89 % Favored : 91.89 % Rotamer: Outliers : 5.36 % Allowed : 13.26 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.13), residues: 2700 helix: -1.90 (0.11), residues: 1544 sheet: -1.41 (0.72), residues: 42 loop : -3.29 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.027 0.002 TYR C 385 PHE 0.014 0.002 PHE D 549 TRP 0.017 0.002 TRP C 566 HIS 0.008 0.002 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01274 / 0.58 (22948) covalent geometry : angle 0.93397 / 0.54 (31236) SS BOND : bond 0.00482 / 0.33 ( 10) SS BOND : angle 2.46164 / 1.76 ( 20) hydrogen bonds : bond 0.17775 / 11.70 ( 1083) hydrogen bonds : angle 7.08903 / 4.96 ( 3189) metal coordination : bond 0.27935 / 13.10 ( 4) Misc. bond : bond 0.21172 / 10.62 ( 2) link_BETA1-4 : bond 0.00909 / 0.58 ( 14) link_BETA1-4 : angle 2.62525 / 1.82 ( 42) link_NAG-ASN : bond 0.00742 / 0.48 ( 24) link_NAG-ASN : angle 3.36896 / 2.40 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 286 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (m-40) REVERT: A 735 ASN cc_start: 0.6752 (OUTLIER) cc_final: 0.6357 (p0) REVERT: A 766 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3997 (ttt180) REVERT: C 290 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8649 (m-40) REVERT: C 735 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6344 (p0) REVERT: C 766 ARG cc_start: 0.4808 (OUTLIER) cc_final: 0.4133 (ttt180) outliers start: 128 outliers final: 38 residues processed: 406 average time/residue: 0.1329 time to fit residues: 87.6713 Evaluate side-chains 196 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 ASN Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 766 ARG Chi-restraints excluded: chain D residue 129 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 63 ASN A 101 GLN A 239 HIS A 250 ASN A 277 ASN A 373 HIS A 493 HIS A 556 ASN A 586 ASN A 599 ASN A 682 ASN A 735 ASN B 194 GLN B 435 ASN B 444 GLN C 33 ASN C 63 ASN C 101 GLN C 239 HIS C 250 ASN C 277 ASN C 373 HIS C 493 HIS C 556 ASN C 586 ASN C 599 ASN C 682 ASN C 735 ASN D 194 GLN D 435 ASN D 444 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.122604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076281 restraints weight = 47424.624| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.54 r_work: 0.2938 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23002 Z= 0.145 Angle : 0.702 12.609 31370 Z= 0.349 Chirality : 0.044 0.262 3528 Planarity : 0.004 0.052 3914 Dihedral : 7.500 82.746 3000 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 3.60 % Allowed : 16.44 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 2700 helix: -0.25 (0.13), residues: 1580 sheet: -1.47 (0.60), residues: 62 loop : -2.49 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 245 TYR 0.017 0.001 TYR B 567 PHE 0.020 0.001 PHE B 283 TRP 0.018 0.001 TRP B 104 HIS 0.005 0.001 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (22948) covalent geometry : angle 0.68484 / 0.34 (31236) SS BOND : bond 0.00940 / 0.56 ( 10) SS BOND : angle 2.63378 / 1.61 ( 20) hydrogen bonds : bond 0.05383 / 3.52 ( 1083) hydrogen bonds : angle 4.82820 / 3.37 ( 3189) metal coordination : bond 0.00756 / 0.35 ( 4) Misc. bond : bond 0.00326 / 0.16 ( 2) link_BETA1-4 : bond 0.00427 / 0.28 ( 14) link_BETA1-4 : angle 1.74336 / 1.16 ( 42) link_NAG-ASN : bond 0.00966 / 0.72 ( 24) link_NAG-ASN : angle 2.73814 / 1.99 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 189 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8637 (m-40) REVERT: A 297 MET cc_start: 0.8742 (ttm) cc_final: 0.8477 (mtp) REVERT: A 596 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8854 (mtmt) REVERT: A 766 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.3856 (ttt180) REVERT: B 36 ASP cc_start: 0.7367 (m-30) cc_final: 0.7134 (t0) REVERT: B 71 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7063 (mmm) REVERT: B 137 MET cc_start: 0.9074 (mtp) cc_final: 0.8857 (mtp) REVERT: B 435 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7142 (m110) REVERT: B 502 MET cc_start: 0.7161 (tmm) cc_final: 0.6905 (ttp) REVERT: C 290 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (m-40) REVERT: C 297 MET cc_start: 0.8745 (ttm) cc_final: 0.8480 (mtp) REVERT: C 596 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8853 (mtmt) REVERT: C 766 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.3848 (ttt180) REVERT: D 36 ASP cc_start: 0.7318 (m-30) cc_final: 0.7115 (t0) REVERT: D 128 TYR cc_start: 0.6297 (t80) cc_final: 0.5409 (t80) REVERT: D 137 MET cc_start: 0.9075 (mtp) cc_final: 0.8857 (mtp) REVERT: D 435 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7144 (m110) outliers start: 86 outliers final: 31 residues processed: 267 average time/residue: 0.1320 time to fit residues: 57.9505 Evaluate side-chains 172 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 766 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 516 LYS Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 168 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 139 GLN B 435 ASN B 444 GLN C 139 GLN D 435 ASN D 444 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074274 restraints weight = 46616.693| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.48 r_work: 0.2892 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23002 Z= 0.195 Angle : 0.670 8.659 31370 Z= 0.335 Chirality : 0.045 0.240 3528 Planarity : 0.004 0.036 3914 Dihedral : 6.213 81.610 2950 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 3.72 % Allowed : 16.32 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2700 helix: 0.28 (0.13), residues: 1578 sheet: -1.33 (0.59), residues: 62 loop : -2.09 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.016 0.001 TYR A 183 PHE 0.014 0.001 PHE D 283 TRP 0.011 0.001 TRP C 165 HIS 0.006 0.001 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (22948) covalent geometry : angle 0.65263 / 0.33 (31236) SS BOND : bond 0.01378 / 0.81 ( 10) SS BOND : angle 3.14460 / 1.96 ( 20) hydrogen bonds : bond 0.05207 / 3.36 ( 1083) hydrogen bonds : angle 4.56349 / 3.20 ( 3189) metal coordination : bond 0.00325 / 0.15 ( 4) Misc. bond : bond 0.00133 / 0.07 ( 2) link_BETA1-4 : bond 0.00279 / 0.20 ( 14) link_BETA1-4 : angle 1.77105 / 1.18 ( 42) link_NAG-ASN : bond 0.00417 / 0.29 ( 24) link_NAG-ASN : angle 2.50612 / 1.84 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 146 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7599 (m90) REVERT: A 60 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: A 171 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: A 290 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8704 (m-40) REVERT: A 297 MET cc_start: 0.8775 (ttm) cc_final: 0.8384 (mtp) REVERT: A 722 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8880 (tp) REVERT: A 760 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6314 (mm) REVERT: B 28 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: B 36 ASP cc_start: 0.7382 (m-30) cc_final: 0.7014 (t0) REVERT: B 137 MET cc_start: 0.9087 (mtp) cc_final: 0.8845 (mtp) REVERT: B 435 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7366 (m110) REVERT: B 550 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 60 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: C 171 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 290 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8673 (m-40) REVERT: C 297 MET cc_start: 0.8741 (ttm) cc_final: 0.8334 (mtp) REVERT: D 28 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5715 (pt0) REVERT: D 36 ASP cc_start: 0.7375 (m-30) cc_final: 0.7011 (t0) REVERT: D 137 MET cc_start: 0.9086 (mtp) cc_final: 0.8843 (mtp) REVERT: D 435 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7373 (m110) REVERT: D 550 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7247 (t80) outliers start: 89 outliers final: 47 residues processed: 228 average time/residue: 0.1283 time to fit residues: 48.2769 Evaluate side-chains 189 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 221 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 208 optimal weight: 0.0670 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 182 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 522 GLN B 296 HIS B 435 ASN B 524 HIS C 522 GLN D 296 HIS D 435 ASN D 524 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.121625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076747 restraints weight = 46275.288| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.49 r_work: 0.2946 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23002 Z= 0.114 Angle : 0.605 11.437 31370 Z= 0.299 Chirality : 0.042 0.210 3528 Planarity : 0.004 0.034 3914 Dihedral : 5.730 75.196 2942 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 2.55 % Allowed : 17.49 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2700 helix: 0.61 (0.14), residues: 1606 sheet: -1.39 (0.58), residues: 62 loop : -1.93 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.011 0.001 TYR D 60 PHE 0.024 0.001 PHE B 548 TRP 0.013 0.001 TRP A 742 HIS 0.017 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22948) covalent geometry : angle 0.58757 / 0.29 (31236) SS BOND : bond 0.00742 / 0.43 ( 10) SS BOND : angle 3.09040 / 1.84 ( 20) hydrogen bonds : bond 0.04271 / 2.75 ( 1083) hydrogen bonds : angle 4.31005 / 3.01 ( 3189) metal coordination : bond 0.00023 / 0.01 ( 4) Misc. bond : bond 0.00032 / 0.02 ( 2) link_BETA1-4 : bond 0.00396 / 0.26 ( 14) link_BETA1-4 : angle 1.66017 / 1.11 ( 42) link_NAG-ASN : bond 0.00455 / 0.30 ( 24) link_NAG-ASN : angle 2.32584 / 1.70 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.841 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 60 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: A 171 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: A 290 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8642 (m-40) REVERT: A 297 MET cc_start: 0.8740 (ttm) cc_final: 0.8409 (mtp) REVERT: A 474 MET cc_start: 0.9081 (mmm) cc_final: 0.8836 (mmm) REVERT: A 596 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8805 (mtmt) REVERT: A 760 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6157 (mm) REVERT: B 28 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: B 71 MET cc_start: 0.7968 (tpp) cc_final: 0.7512 (mmp) REVERT: B 137 MET cc_start: 0.9076 (mtp) cc_final: 0.8588 (mtp) REVERT: B 435 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7353 (m110) REVERT: B 518 ILE cc_start: 0.9401 (mm) cc_final: 0.9070 (tp) REVERT: B 550 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 60 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: C 171 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 290 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8638 (m-40) REVERT: C 297 MET cc_start: 0.8752 (ttm) cc_final: 0.8421 (mtp) REVERT: C 474 MET cc_start: 0.9082 (mmm) cc_final: 0.8835 (mmm) REVERT: C 596 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8807 (mtmt) REVERT: C 722 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 28 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5728 (pt0) REVERT: D 71 MET cc_start: 0.7976 (tpp) cc_final: 0.7503 (mmp) REVERT: D 137 MET cc_start: 0.9073 (mtp) cc_final: 0.8580 (mtp) REVERT: D 435 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7351 (m110) REVERT: D 518 ILE cc_start: 0.9402 (mm) cc_final: 0.9060 (tp) REVERT: D 550 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7215 (t80) outliers start: 61 outliers final: 33 residues processed: 204 average time/residue: 0.1191 time to fit residues: 40.6309 Evaluate side-chains 188 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 550 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 56 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 184 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 208 optimal weight: 0.0770 chunk 85 optimal weight: 5.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS B 435 ASN B 524 HIS D 63 GLN D 435 ASN D 524 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.120805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075896 restraints weight = 45950.898| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.48 r_work: 0.2912 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23002 Z= 0.138 Angle : 0.599 11.621 31370 Z= 0.295 Chirality : 0.042 0.171 3528 Planarity : 0.004 0.033 3914 Dihedral : 5.522 73.171 2938 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 2.89 % Allowed : 18.24 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2700 helix: 0.80 (0.14), residues: 1608 sheet: -1.33 (0.59), residues: 62 loop : -1.83 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR B 60 PHE 0.014 0.001 PHE B 548 TRP 0.014 0.001 TRP A 742 HIS 0.008 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22948) covalent geometry : angle 0.58437 / 0.29 (31236) SS BOND : bond 0.00636 / 0.37 ( 10) SS BOND : angle 2.45556 / 1.41 ( 20) hydrogen bonds : bond 0.04358 / 2.81 ( 1083) hydrogen bonds : angle 4.20862 / 2.95 ( 3189) metal coordination : bond 0.00169 / 0.08 ( 4) Misc. bond : bond 0.00033 / 0.02 ( 2) link_BETA1-4 : bond 0.00381 / 0.26 ( 14) link_BETA1-4 : angle 1.65300 / 1.10 ( 42) link_NAG-ASN : bond 0.00363 / 0.25 ( 24) link_NAG-ASN : angle 2.25953 / 1.67 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 144 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: A 297 MET cc_start: 0.8817 (ttm) cc_final: 0.8494 (mtp) REVERT: A 474 MET cc_start: 0.9204 (mmm) cc_final: 0.8917 (mmm) REVERT: A 760 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6353 (mm) REVERT: B 28 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5769 (pt0) REVERT: B 71 MET cc_start: 0.7913 (tpp) cc_final: 0.7471 (mmp) REVERT: B 435 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7119 (m110) REVERT: B 518 ILE cc_start: 0.9404 (mm) cc_final: 0.9074 (tp) REVERT: B 550 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7207 (t80) REVERT: C 171 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: C 290 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8718 (m-40) REVERT: C 297 MET cc_start: 0.8822 (ttm) cc_final: 0.8498 (mtp) REVERT: C 474 MET cc_start: 0.9207 (mmm) cc_final: 0.8921 (mmm) REVERT: C 722 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8942 (tp) REVERT: C 760 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6382 (mm) REVERT: D 28 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5751 (pt0) REVERT: D 71 MET cc_start: 0.7998 (tpp) cc_final: 0.7421 (mmp) REVERT: D 435 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7124 (m110) REVERT: D 518 ILE cc_start: 0.9402 (mm) cc_final: 0.9059 (tp) REVERT: D 550 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7208 (t80) outliers start: 69 outliers final: 46 residues processed: 205 average time/residue: 0.1186 time to fit residues: 39.9963 Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 132 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL 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 365 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 573 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 246 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 133 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 ASN B 524 HIS D 435 ASN D 524 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075833 restraints weight = 46318.046| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.51 r_work: 0.2926 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23002 Z= 0.121 Angle : 0.592 11.917 31370 Z= 0.289 Chirality : 0.042 0.178 3528 Planarity : 0.004 0.034 3914 Dihedral : 4.967 59.208 2930 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.26 % Allowed : 17.99 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2700 helix: 0.96 (0.14), residues: 1612 sheet: -1.36 (0.58), residues: 62 loop : -1.81 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.011 0.001 TYR A 183 PHE 0.022 0.001 PHE D 548 TRP 0.016 0.001 TRP A 742 HIS 0.008 0.001 HIS B 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22948) covalent geometry : angle 0.57902 / 0.29 (31236) SS BOND : bond 0.00812 / 0.47 ( 10) SS BOND : angle 2.00391 / 1.15 ( 20) hydrogen bonds : bond 0.04090 / 2.63 ( 1083) hydrogen bonds : angle 4.13837 / 2.89 ( 3189) metal coordination : bond 0.00108 / 0.05 ( 4) Misc. bond : bond 0.00413 / 0.21 ( 2) link_BETA1-4 : bond 0.00349 / 0.23 ( 14) link_BETA1-4 : angle 1.57809 / 1.06 ( 42) link_NAG-ASN : bond 0.00369 / 0.25 ( 24) link_NAG-ASN : angle 2.17863 / 1.61 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 135 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 297 MET cc_start: 0.8820 (ttm) cc_final: 0.8466 (mtp) REVERT: A 474 MET cc_start: 0.9206 (mmm) cc_final: 0.8951 (mmm) REVERT: A 722 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8910 (tp) REVERT: A 760 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6262 (mm) REVERT: B 28 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5744 (pt0) REVERT: B 71 MET cc_start: 0.7955 (tpp) cc_final: 0.7520 (mmp) REVERT: B 435 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7066 (m110) REVERT: B 502 MET cc_start: 0.7085 (tpp) cc_final: 0.6219 (ttp) REVERT: B 518 ILE cc_start: 0.9399 (mm) cc_final: 0.9062 (tp) REVERT: B 550 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 552 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7723 (m) REVERT: C 171 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: C 297 MET cc_start: 0.8791 (ttm) cc_final: 0.8429 (mtp) REVERT: C 474 MET cc_start: 0.9204 (mmm) cc_final: 0.8950 (mmm) REVERT: C 722 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8892 (tp) REVERT: C 760 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6256 (mm) REVERT: D 28 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: D 71 MET cc_start: 0.7981 (tpp) cc_final: 0.7399 (mmp) REVERT: D 435 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7070 (m110) REVERT: D 518 ILE cc_start: 0.9410 (mm) cc_final: 0.9067 (tp) REVERT: D 550 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7222 (t80) REVERT: D 552 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7732 (m) outliers start: 78 outliers final: 48 residues processed: 205 average time/residue: 0.1285 time to fit residues: 43.2897 Evaluate side-chains 182 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 GLN B 435 ASN C 117 ASN C 616 GLN D 435 ASN D 524 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074666 restraints weight = 46521.860| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.52 r_work: 0.2892 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23002 Z= 0.169 Angle : 0.649 20.315 31370 Z= 0.319 Chirality : 0.044 0.404 3528 Planarity : 0.004 0.033 3914 Dihedral : 4.948 59.198 2928 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.39 % Allowed : 17.66 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2700 helix: 0.99 (0.14), residues: 1612 sheet: -1.19 (0.59), residues: 62 loop : -1.74 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.015 0.001 TYR A 183 PHE 0.026 0.001 PHE B 548 TRP 0.017 0.001 TRP A 742 HIS 0.009 0.001 HIS D 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (22948) covalent geometry : angle 0.62929 / 0.31 (31236) SS BOND : bond 0.00891 / 0.52 ( 10) SS BOND : angle 4.65204 / 3.10 ( 20) hydrogen bonds : bond 0.04362 / 2.81 ( 1083) hydrogen bonds : angle 4.16632 / 2.91 ( 3189) metal coordination : bond 0.00264 / 0.13 ( 4) Misc. bond : bond 0.00491 / 0.25 ( 2) link_BETA1-4 : bond 0.00371 / 0.25 ( 14) link_BETA1-4 : angle 1.55798 / 1.05 ( 42) link_NAG-ASN : bond 0.00377 / 0.27 ( 24) link_NAG-ASN : angle 2.13351 / 1.58 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 126 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 297 MET cc_start: 0.8840 (ttm) cc_final: 0.8478 (mtp) REVERT: A 474 MET cc_start: 0.9234 (mmm) cc_final: 0.8937 (mmm) REVERT: A 722 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 760 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6272 (mm) REVERT: B 28 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5749 (pt0) REVERT: B 71 MET cc_start: 0.7883 (tpp) cc_final: 0.7230 (mmp) REVERT: B 137 MET cc_start: 0.9102 (mtp) cc_final: 0.8821 (mtp) REVERT: B 331 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 518 ILE cc_start: 0.9407 (mm) cc_final: 0.9071 (tp) REVERT: B 550 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 552 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7735 (m) REVERT: C 171 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 297 MET cc_start: 0.8837 (ttm) cc_final: 0.8479 (mtp) REVERT: C 474 MET cc_start: 0.9228 (mmm) cc_final: 0.8934 (mmm) REVERT: C 722 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8960 (tp) REVERT: C 760 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6253 (mm) REVERT: D 28 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5742 (pt0) REVERT: D 71 MET cc_start: 0.7935 (tpp) cc_final: 0.7332 (mmp) REVERT: D 137 MET cc_start: 0.9105 (mtp) cc_final: 0.8822 (mtp) REVERT: D 331 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 516 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9054 (ptpp) REVERT: D 518 ILE cc_start: 0.9411 (mm) cc_final: 0.9070 (tp) REVERT: D 550 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7321 (t80) REVERT: D 552 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7718 (m) outliers start: 81 outliers final: 52 residues processed: 196 average time/residue: 0.1143 time to fit residues: 38.1404 Evaluate side-chains 191 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 243 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 ASN D 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075000 restraints weight = 46344.066| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.50 r_work: 0.2898 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23002 Z= 0.148 Angle : 0.634 17.846 31370 Z= 0.312 Chirality : 0.043 0.361 3528 Planarity : 0.004 0.034 3914 Dihedral : 4.906 59.444 2924 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.97 % Allowed : 18.20 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.17), residues: 2700 helix: 1.07 (0.14), residues: 1614 sheet: -1.13 (0.59), residues: 62 loop : -1.70 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 447 TYR 0.014 0.001 TYR A 183 PHE 0.019 0.001 PHE B 548 TRP 0.020 0.001 TRP C 742 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (22948) covalent geometry : angle 0.61278 / 0.30 (31236) SS BOND : bond 0.01244 / 0.72 ( 10) SS BOND : angle 4.87636 / 3.25 ( 20) hydrogen bonds : bond 0.04249 / 2.74 ( 1083) hydrogen bonds : angle 4.13805 / 2.89 ( 3189) metal coordination : bond 0.00173 / 0.08 ( 4) Misc. bond : bond 0.00562 / 0.28 ( 2) link_BETA1-4 : bond 0.00353 / 0.24 ( 14) link_BETA1-4 : angle 1.51197 / 1.02 ( 42) link_NAG-ASN : bond 0.00360 / 0.26 ( 24) link_NAG-ASN : angle 2.04555 / 1.51 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 128 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 297 MET cc_start: 0.8891 (ttm) cc_final: 0.8552 (mtp) REVERT: A 474 MET cc_start: 0.9237 (mmm) cc_final: 0.8965 (mmm) REVERT: A 722 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8912 (tp) REVERT: A 760 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6259 (mm) REVERT: B 28 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5796 (pt0) REVERT: B 137 MET cc_start: 0.9108 (mtp) cc_final: 0.8857 (mtp) REVERT: B 331 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 435 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7274 (m110) REVERT: B 518 ILE cc_start: 0.9385 (mm) cc_final: 0.9057 (tp) REVERT: B 550 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 552 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7751 (m) REVERT: C 171 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: C 297 MET cc_start: 0.8885 (ttm) cc_final: 0.8545 (mtp) REVERT: C 474 MET cc_start: 0.9228 (mmm) cc_final: 0.8957 (mmm) REVERT: C 722 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8926 (tp) REVERT: C 760 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6201 (mm) REVERT: D 28 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5792 (pt0) REVERT: D 137 MET cc_start: 0.9113 (mtp) cc_final: 0.8871 (mtp) REVERT: D 331 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 435 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7311 (m110) REVERT: D 502 MET cc_start: 0.7197 (tmm) cc_final: 0.6860 (ttp) REVERT: D 516 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (ptpp) REVERT: D 518 ILE cc_start: 0.9399 (mm) cc_final: 0.9062 (tp) REVERT: D 550 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7346 (t80) REVERT: D 552 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7742 (m) outliers start: 71 outliers final: 51 residues processed: 190 average time/residue: 0.1272 time to fit residues: 41.1118 Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 516 LYS Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.074078 restraints weight = 47326.411| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.56 r_work: 0.2889 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23002 Z= 0.156 Angle : 0.628 15.831 31370 Z= 0.310 Chirality : 0.043 0.309 3528 Planarity : 0.004 0.032 3914 Dihedral : 4.876 59.393 2924 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.97 % Allowed : 18.33 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.17), residues: 2700 helix: 1.10 (0.14), residues: 1614 sheet: -1.16 (0.57), residues: 66 loop : -1.69 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.014 0.001 TYR A 183 PHE 0.027 0.001 PHE D 548 TRP 0.021 0.001 TRP A 742 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (22948) covalent geometry : angle 0.60947 / 0.30 (31236) SS BOND : bond 0.00736 / 0.43 ( 10) SS BOND : angle 4.50029 / 2.98 ( 20) hydrogen bonds : bond 0.04311 / 2.78 ( 1083) hydrogen bonds : angle 4.08436 / 2.85 ( 3189) metal coordination : bond 0.00229 / 0.11 ( 4) Misc. bond : bond 0.00526 / 0.26 ( 2) link_BETA1-4 : bond 0.00375 / 0.26 ( 14) link_BETA1-4 : angle 1.49359 / 1.01 ( 42) link_NAG-ASN : bond 0.00356 / 0.26 ( 24) link_NAG-ASN : angle 1.99845 / 1.48 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8272 (tp) REVERT: A 171 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: A 297 MET cc_start: 0.8934 (ttm) cc_final: 0.8606 (mtp) REVERT: A 474 MET cc_start: 0.9257 (mmm) cc_final: 0.8950 (mmm) REVERT: A 596 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8882 (mtmt) REVERT: A 722 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 760 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6310 (mm) REVERT: B 28 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5787 (pt0) REVERT: B 137 MET cc_start: 0.9129 (mtp) cc_final: 0.8907 (mtp) REVERT: B 518 ILE cc_start: 0.9392 (mm) cc_final: 0.9065 (tp) REVERT: B 550 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7385 (t80) REVERT: B 552 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (m) REVERT: C 171 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: C 297 MET cc_start: 0.8916 (ttm) cc_final: 0.8622 (mtp) REVERT: C 474 MET cc_start: 0.9249 (mmm) cc_final: 0.8943 (mmm) REVERT: C 596 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8889 (mtmt) REVERT: C 722 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8963 (tp) REVERT: C 760 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6255 (mm) REVERT: D 28 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5775 (pt0) REVERT: D 137 MET cc_start: 0.9133 (mtp) cc_final: 0.8909 (mtp) REVERT: D 502 MET cc_start: 0.7186 (tmm) cc_final: 0.6863 (ttp) REVERT: D 550 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7360 (t80) REVERT: D 552 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7739 (m) outliers start: 71 outliers final: 52 residues processed: 192 average time/residue: 0.1266 time to fit residues: 41.4824 Evaluate side-chains 189 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 122 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 HIS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 260 optimal weight: 6.9990 chunk 140 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 206 optimal weight: 0.0370 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS B 435 ASN D 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.121245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.076184 restraints weight = 47517.091| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.59 r_work: 0.2935 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23002 Z= 0.106 Angle : 0.600 14.542 31370 Z= 0.296 Chirality : 0.042 0.268 3528 Planarity : 0.003 0.033 3914 Dihedral : 4.709 58.276 2924 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.47 % Allowed : 18.83 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2700 helix: 1.21 (0.14), residues: 1626 sheet: -1.26 (0.55), residues: 66 loop : -1.65 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 161 TYR 0.010 0.001 TYR D 60 PHE 0.022 0.001 PHE D 548 TRP 0.023 0.001 TRP C 742 HIS 0.021 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (22948) covalent geometry : angle 0.58233 / 0.29 (31236) SS BOND : bond 0.00603 / 0.35 ( 10) SS BOND : angle 4.19326 / 2.80 ( 20) hydrogen bonds : bond 0.03803 / 2.43 ( 1083) hydrogen bonds : angle 4.00446 / 2.79 ( 3189) metal coordination : bond 0.00040 / 0.02 ( 4) Misc. bond : bond 0.00378 / 0.19 ( 2) link_BETA1-4 : bond 0.00399 / 0.26 ( 14) link_BETA1-4 : angle 1.44723 / 0.98 ( 42) link_NAG-ASN : bond 0.00374 / 0.25 ( 24) link_NAG-ASN : angle 1.92400 / 1.42 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8620 (pmm) cc_final: 0.8353 (pmm) REVERT: A 171 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 297 MET cc_start: 0.8934 (ttm) cc_final: 0.8603 (mtp) REVERT: A 596 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8838 (mtmt) REVERT: A 760 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6363 (mm) REVERT: B 28 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5808 (pt0) REVERT: B 71 MET cc_start: 0.8004 (tpp) cc_final: 0.7516 (mmp) REVERT: B 455 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5506 (pttp) REVERT: B 518 ILE cc_start: 0.9378 (mm) cc_final: 0.9047 (tp) REVERT: B 550 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 552 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7743 (m) REVERT: C 82 MET cc_start: 0.8629 (pmm) cc_final: 0.8356 (pmm) REVERT: C 171 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: C 297 MET cc_start: 0.8928 (ttm) cc_final: 0.8596 (mtp) REVERT: C 596 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8841 (mtmt) REVERT: C 722 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 760 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6331 (mm) REVERT: D 28 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5780 (pt0) REVERT: D 71 MET cc_start: 0.7904 (tpp) cc_final: 0.7373 (mmp) REVERT: D 455 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5520 (pttp) REVERT: D 502 MET cc_start: 0.7189 (tmm) cc_final: 0.6917 (ttp) REVERT: D 550 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7391 (t80) REVERT: D 552 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7745 (m) outliers start: 59 outliers final: 37 residues processed: 183 average time/residue: 0.1330 time to fit residues: 40.9888 Evaluate side-chains 175 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 HIS Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 383 CYS Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 165 optimal weight: 0.2980 chunk 255 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.121200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077956 restraints weight = 47406.428| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.00 r_work: 0.2912 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23002 Z= 0.107 Angle : 0.584 13.542 31370 Z= 0.286 Chirality : 0.041 0.250 3528 Planarity : 0.003 0.031 3914 Dihedral : 4.591 57.030 2924 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.22 % Allowed : 19.21 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2700 helix: 1.27 (0.14), residues: 1636 sheet: -1.18 (0.56), residues: 66 loop : -1.56 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 14 TYR 0.010 0.001 TYR D 60 PHE 0.023 0.001 PHE B 548 TRP 0.023 0.001 TRP D 104 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (22948) covalent geometry : angle 0.56616 / 0.28 (31236) SS BOND : bond 0.00412 / 0.24 ( 10) SS BOND : angle 4.06946 / 2.71 ( 20) hydrogen bonds : bond 0.03691 / 2.36 ( 1083) hydrogen bonds : angle 3.92789 / 2.74 ( 3189) metal coordination : bond 0.00084 / 0.04 ( 4) Misc. bond : bond 0.00393 / 0.20 ( 2) link_BETA1-4 : bond 0.00367 / 0.25 ( 14) link_BETA1-4 : angle 1.42412 / 0.96 ( 42) link_NAG-ASN : bond 0.00321 / 0.22 ( 24) link_NAG-ASN : angle 1.87353 / 1.38 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6889.75 seconds wall clock time: 118 minutes 12.02 seconds (7092.02 seconds total)