Starting phenix.real_space_refine on Thu Jun 19 09:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i92_35255/06_2025/8i92_35255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i92_35255/06_2025/8i92_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_35255/06_2025/8i92_35255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i92_35255/06_2025/8i92_35255.map" model { file = "/net/cci-nas-00/data/ceres_data/8i92_35255/06_2025/8i92_35255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i92_35255/06_2025/8i92_35255.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.64, per 1000 atoms: 0.57 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: 5.80 Conformation dependent library (CDL) restraints added in 2.6 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: 2.39 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: 7.36 Time building geometry restraints manager: 6.81 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: 12217 17.98 - 35.96: 1236 35.96 - 53.95: 380 53.95 - 71.93: 83 71.93 - 89.91: 32 Dihedral angle restraints: 13948 sinusoidal: 6038 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 13945 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 52.830 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 16.448 89.908 8830 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP C 566 HIS 0.008 0.002 HIS C 241 PHE 0.014 0.002 PHE D 549 TYR 0.027 0.002 TYR C 385 ARG 0.004 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 24) link_NAG-ASN : angle 3.36896 ( 72) link_BETA1-4 : bond 0.00909 ( 14) link_BETA1-4 : angle 2.62525 ( 42) hydrogen bonds : bond 0.17775 ( 1083) hydrogen bonds : angle 7.08903 ( 3189) metal coordination : bond 0.27935 ( 4) SS BOND : bond 0.00482 ( 10) SS BOND : angle 2.46164 ( 20) covalent geometry : bond 0.01274 (22948) covalent geometry : angle 0.93397 (31236) Misc. bond : bond 0.21172 ( 2) *********************** 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 : 2.315 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: 0.6354 (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: 0.6341 (p0) REVERT: C 766 ARG cc_start: 0.4808 (OUTLIER) cc_final: 0.4132 (ttt180) outliers start: 128 outliers final: 38 residues processed: 406 average time/residue: 0.2989 time to fit residues: 195.6547 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 : 2.691 ------------------------------------------------------------------------------- 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 226 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 chunk 210 optimal weight: 0.0040 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 243 optimal weight: 8.9990 overall best weight: 0.5450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3924 r_free = 0.3924 target = 0.122648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.078567 restraints weight = 47076.790| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.77 r_work: 0.2937 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23002 Z= 0.143 Angle : 0.705 12.711 31370 Z= 0.350 Chirality : 0.044 0.333 3528 Planarity : 0.004 0.051 3914 Dihedral : 8.735 82.923 3798 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 3.77 % Allowed : 16.49 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 2700 helix: -0.31 (0.13), residues: 1594 sheet: -1.49 (0.60), residues: 62 loop : -2.52 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.005 0.001 HIS D 65 PHE 0.020 0.001 PHE B 283 TYR 0.018 0.001 TYR D 567 ARG 0.004 0.000 ARG C 768 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 24) link_NAG-ASN : angle 2.70487 ( 72) link_BETA1-4 : bond 0.00447 ( 14) link_BETA1-4 : angle 1.87204 ( 42) hydrogen bonds : bond 0.05410 ( 1083) hydrogen bonds : angle 4.83682 ( 3189) metal coordination : bond 0.01409 ( 4) SS BOND : bond 0.00757 ( 10) SS BOND : angle 2.61753 ( 20) covalent geometry : bond 0.00293 (22948) covalent geometry : angle 0.68749 (31236) Misc. bond : bond 0.01768 ( 2) *********************** 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 280 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7613 (m90) REVERT: A 290 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8643 (m-40) REVERT: A 297 MET cc_start: 0.8730 (ttm) cc_final: 0.8469 (mtp) REVERT: A 596 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8857 (mtmt) REVERT: A 766 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.3878 (ttt180) REVERT: B 36 ASP cc_start: 0.7363 (m-30) cc_final: 0.7122 (t0) REVERT: B 137 MET cc_start: 0.9072 (mtp) cc_final: 0.8858 (mtp) REVERT: B 435 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.6994 (m-40) REVERT: B 502 MET cc_start: 0.7175 (tmm) cc_final: 0.6827 (ttp) REVERT: C 105 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (t) REVERT: C 290 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: C 297 MET cc_start: 0.8733 (ttm) cc_final: 0.8473 (mtp) REVERT: C 596 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8851 (mtmt) REVERT: C 766 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.3983 (ttt180) REVERT: D 36 ASP cc_start: 0.7314 (m-30) cc_final: 0.7111 (t0) REVERT: D 128 TYR cc_start: 0.6288 (t80) cc_final: 0.5395 (t80) REVERT: D 137 MET cc_start: 0.9072 (mtp) cc_final: 0.8859 (mtp) REVERT: D 435 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.6978 (m-40) REVERT: D 502 MET cc_start: 0.7141 (tmm) cc_final: 0.6913 (ttp) outliers start: 90 outliers final: 33 residues processed: 273 average time/residue: 0.3241 time to fit residues: 146.2677 Evaluate side-chains 181 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 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 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 464 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 105 SER 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 464 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 160 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075106 restraints weight = 45921.131| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.47 r_work: 0.2905 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23002 Z= 0.177 Angle : 0.656 8.403 31370 Z= 0.328 Chirality : 0.044 0.195 3528 Planarity : 0.004 0.038 3914 Dihedral : 7.074 82.046 3749 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 16.86 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2700 helix: 0.33 (0.13), residues: 1578 sheet: -1.33 (0.59), residues: 62 loop : -2.05 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 104 HIS 0.005 0.001 HIS B 65 PHE 0.015 0.001 PHE B 283 TYR 0.015 0.001 TYR A 183 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 24) link_NAG-ASN : angle 2.41961 ( 72) link_BETA1-4 : bond 0.00398 ( 14) link_BETA1-4 : angle 1.91411 ( 42) hydrogen bonds : bond 0.05039 ( 1083) hydrogen bonds : angle 4.49767 ( 3189) metal coordination : bond 0.00401 ( 4) SS BOND : bond 0.00842 ( 10) SS BOND : angle 2.40575 ( 20) covalent geometry : bond 0.00413 (22948) covalent geometry : angle 0.64021 (31236) Misc. bond : bond 0.00099 ( 2) *********************** 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 234 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 148 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: A 171 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 290 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8695 (m-40) REVERT: A 297 MET cc_start: 0.8709 (ttm) cc_final: 0.8320 (mtp) REVERT: B 28 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5713 (pt0) REVERT: B 137 MET cc_start: 0.9088 (mtp) cc_final: 0.8846 (mtp) REVERT: B 435 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7537 (m110) REVERT: B 550 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 60 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: C 171 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: C 290 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: C 297 MET cc_start: 0.8720 (ttm) cc_final: 0.8326 (mtp) REVERT: D 28 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5761 (pt0) REVERT: D 137 MET cc_start: 0.9072 (mtp) cc_final: 0.8821 (mtp) REVERT: D 435 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7553 (m110) REVERT: D 502 MET cc_start: 0.7126 (tmm) cc_final: 0.6663 (tmm) REVERT: D 518 ILE cc_start: 0.9369 (mm) cc_final: 0.9019 (tp) REVERT: D 550 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7250 (t80) outliers start: 86 outliers final: 47 residues processed: 226 average time/residue: 0.3267 time to fit residues: 123.9323 Evaluate side-chains 187 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 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 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 749 VAL 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 439 VAL Chi-restraints excluded: chain B residue 455 LYS 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 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 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 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 725 LEU 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 439 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 550 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 175 optimal weight: 0.0870 chunk 96 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 296 HIS B 435 ASN B 524 HIS C 34 HIS D 296 HIS D 435 ASN D 524 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.120011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074995 restraints weight = 46431.740| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.49 r_work: 0.2909 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2970 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= 0.146 Angle : 0.630 11.093 31370 Z= 0.312 Chirality : 0.043 0.210 3528 Planarity : 0.004 0.035 3914 Dihedral : 6.506 75.831 3740 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.68 % Allowed : 18.08 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2700 helix: 0.57 (0.13), residues: 1602 sheet: -1.26 (0.60), residues: 62 loop : -1.92 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 742 HIS 0.008 0.001 HIS B 524 PHE 0.013 0.001 PHE B 548 TYR 0.014 0.001 TYR D 60 ARG 0.002 0.000 ARG C 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 24) link_NAG-ASN : angle 2.35119 ( 72) link_BETA1-4 : bond 0.00385 ( 14) link_BETA1-4 : angle 1.78756 ( 42) hydrogen bonds : bond 0.04586 ( 1083) hydrogen bonds : angle 4.37435 ( 3189) metal coordination : bond 0.00153 ( 4) SS BOND : bond 0.00991 ( 10) SS BOND : angle 3.08306 ( 20) covalent geometry : bond 0.00334 (22948) covalent geometry : angle 0.61258 (31236) Misc. bond : bond 0.00031 ( 2) *********************** 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 208 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: A 171 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 290 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: A 297 MET cc_start: 0.8795 (ttm) cc_final: 0.8469 (mtp) REVERT: A 474 MET cc_start: 0.9194 (mmm) cc_final: 0.8887 (mmm) REVERT: A 562 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9093 (mtpp) REVERT: A 596 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8808 (mtmt) REVERT: A 722 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8870 (tp) REVERT: B 28 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5751 (pt0) REVERT: B 137 MET cc_start: 0.9074 (mtp) cc_final: 0.8587 (mtp) REVERT: B 435 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7394 (m110) REVERT: B 518 ILE cc_start: 0.9402 (mm) cc_final: 0.9067 (tp) REVERT: B 550 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7222 (t80) REVERT: C 60 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: C 171 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: C 290 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: C 297 MET cc_start: 0.8774 (ttm) cc_final: 0.8427 (mtp) REVERT: C 474 MET cc_start: 0.9190 (mmm) cc_final: 0.8881 (mmm) REVERT: C 562 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9092 (mtpp) REVERT: C 596 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8806 (mtmt) REVERT: C 722 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8874 (tp) REVERT: D 28 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5730 (pt0) REVERT: D 137 MET cc_start: 0.9074 (mtp) cc_final: 0.8583 (mtp) REVERT: D 435 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7372 (m110) REVERT: D 518 ILE cc_start: 0.9404 (mm) cc_final: 0.9064 (tp) REVERT: D 550 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7198 (t80) outliers start: 64 outliers final: 39 residues processed: 203 average time/residue: 0.3265 time to fit residues: 109.3340 Evaluate side-chains 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 463 VAL Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 749 VAL 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 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 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 463 VAL Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 722 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN B 524 HIS C 58 ASN D 296 HIS 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 = 0.3892 r_free = 0.3892 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.076075 restraints weight = 46294.579| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.53 r_work: 0.2918 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23002 Z= 0.119 Angle : 0.608 11.876 31370 Z= 0.296 Chirality : 0.041 0.171 3528 Planarity : 0.004 0.033 3914 Dihedral : 6.139 73.148 3736 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 2.89 % Allowed : 18.49 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2700 helix: 0.80 (0.14), residues: 1608 sheet: -1.34 (0.58), residues: 62 loop : -1.85 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 56 HIS 0.009 0.001 HIS D 296 PHE 0.011 0.001 PHE B 123 TYR 0.017 0.001 TYR D 128 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 24) link_NAG-ASN : angle 2.30875 ( 72) link_BETA1-4 : bond 0.00364 ( 14) link_BETA1-4 : angle 1.74220 ( 42) hydrogen bonds : bond 0.04190 ( 1083) hydrogen bonds : angle 4.22080 ( 3189) metal coordination : bond 0.00072 ( 4) SS BOND : bond 0.00570 ( 10) SS BOND : angle 2.27200 ( 20) covalent geometry : bond 0.00265 (22948) covalent geometry : angle 0.59284 (31236) Misc. bond : bond 0.00029 ( 2) *********************** 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 221 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 297 MET cc_start: 0.8800 (ttm) cc_final: 0.8468 (mtp) REVERT: A 474 MET cc_start: 0.9187 (mmm) cc_final: 0.8923 (mmm) REVERT: A 562 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9080 (mtpp) REVERT: A 760 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6372 (mm) REVERT: B 28 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5758 (pt0) REVERT: B 331 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 435 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7185 (m110) REVERT: B 518 ILE cc_start: 0.9397 (mm) cc_final: 0.9061 (tp) REVERT: B 550 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7213 (t80) REVERT: C 171 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 297 MET cc_start: 0.8803 (ttm) cc_final: 0.8498 (mtp) REVERT: C 474 MET cc_start: 0.9184 (mmm) cc_final: 0.8921 (mmm) REVERT: C 562 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9083 (mtpp) REVERT: C 760 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6362 (mm) REVERT: D 28 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5754 (pt0) REVERT: D 331 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 435 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7173 (m110) REVERT: D 518 ILE cc_start: 0.9395 (mm) cc_final: 0.9052 (tp) REVERT: D 550 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7187 (t80) outliers start: 69 outliers final: 44 residues processed: 211 average time/residue: 0.3192 time to fit residues: 109.5079 Evaluate side-chains 193 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 562 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 56 TRP 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 542 MET Chi-restraints excluded: chain B residue 550 PHE 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 330 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 637 ASP 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 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 516 LYS Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 550 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 143 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 GLN B 435 ASN B 524 HIS C 34 HIS C 616 GLN D 435 ASN D 524 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.120058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.074379 restraints weight = 46263.576| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.56 r_work: 0.2899 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23002 Z= 0.153 Angle : 0.624 12.553 31370 Z= 0.306 Chirality : 0.043 0.371 3528 Planarity : 0.004 0.035 3914 Dihedral : 5.591 59.802 3726 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.68 % Allowed : 17.95 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2700 helix: 0.90 (0.13), residues: 1606 sheet: -1.23 (0.59), residues: 62 loop : -1.83 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 56 HIS 0.008 0.001 HIS B 524 PHE 0.022 0.001 PHE D 548 TYR 0.014 0.001 TYR C 183 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 24) link_NAG-ASN : angle 2.26253 ( 72) link_BETA1-4 : bond 0.00352 ( 14) link_BETA1-4 : angle 1.72374 ( 42) hydrogen bonds : bond 0.04330 ( 1083) hydrogen bonds : angle 4.17569 ( 3189) metal coordination : bond 0.00205 ( 4) SS BOND : bond 0.01104 ( 10) SS BOND : angle 3.40524 ( 20) covalent geometry : bond 0.00359 (22948) covalent geometry : angle 0.60651 (31236) Misc. bond : bond 0.00655 ( 2) *********************** 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 223 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 135 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: A 297 MET cc_start: 0.8856 (ttm) cc_final: 0.8496 (mtp) REVERT: A 474 MET cc_start: 0.9210 (mmm) cc_final: 0.8920 (mmm) REVERT: A 562 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9126 (mtpp) REVERT: A 596 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8880 (mtmt) REVERT: A 722 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8950 (tp) REVERT: A 760 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6247 (mm) REVERT: B 28 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5736 (pt0) REVERT: B 435 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7226 (m110) REVERT: B 518 ILE cc_start: 0.9416 (mm) cc_final: 0.9092 (tp) REVERT: B 550 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 552 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7686 (m) REVERT: C 171 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: C 297 MET cc_start: 0.8820 (ttm) cc_final: 0.8456 (mtp) REVERT: C 474 MET cc_start: 0.9207 (mmm) cc_final: 0.8921 (mmm) REVERT: C 562 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9135 (mtpp) REVERT: C 596 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8899 (mtmt) REVERT: C 722 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8954 (tp) REVERT: C 760 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6237 (mm) REVERT: D 28 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5729 (pt0) REVERT: D 435 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7218 (m110) REVERT: D 518 ILE cc_start: 0.9402 (mm) cc_final: 0.9057 (tp) REVERT: D 550 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7241 (t80) REVERT: D 552 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7729 (m) outliers start: 88 outliers final: 53 residues processed: 211 average time/residue: 0.2930 time to fit residues: 101.2978 Evaluate side-chains 197 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 463 VAL Chi-restraints excluded: chain A residue 562 LYS 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 749 VAL 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 56 TRP 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 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 516 LYS Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 552 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 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 562 LYS 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 749 VAL 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 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 516 LYS Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 552 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 96 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 130 optimal weight: 0.0370 chunk 195 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 435 ASN B 524 HIS D 435 ASN D 524 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074788 restraints weight = 46676.551| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.51 r_work: 0.2896 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23002 Z= 0.152 Angle : 0.639 20.581 31370 Z= 0.314 Chirality : 0.044 0.398 3528 Planarity : 0.004 0.033 3914 Dihedral : 5.443 59.710 3726 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.01 % Allowed : 18.66 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2700 helix: 0.96 (0.14), residues: 1612 sheet: -1.18 (0.59), residues: 62 loop : -1.78 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 56 HIS 0.009 0.001 HIS B 524 PHE 0.018 0.001 PHE D 549 TYR 0.014 0.001 TYR C 183 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 24) link_NAG-ASN : angle 2.20963 ( 72) link_BETA1-4 : bond 0.00347 ( 14) link_BETA1-4 : angle 1.69428 ( 42) hydrogen bonds : bond 0.04294 ( 1083) hydrogen bonds : angle 4.16002 ( 3189) metal coordination : bond 0.00219 ( 4) SS BOND : bond 0.01047 ( 10) SS BOND : angle 4.61344 ( 20) covalent geometry : bond 0.00356 (22948) covalent geometry : angle 0.61792 (31236) Misc. bond : bond 0.01001 ( 2) *********************** 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 201 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 129 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 297 MET cc_start: 0.8854 (ttm) cc_final: 0.8497 (mtp) REVERT: A 474 MET cc_start: 0.9220 (mmm) cc_final: 0.8927 (mmm) REVERT: A 562 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9103 (mtpp) REVERT: A 596 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8874 (mtmt) REVERT: A 722 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8948 (tp) REVERT: A 760 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6247 (mm) REVERT: B 28 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5756 (pt0) REVERT: B 137 MET cc_start: 0.9089 (mtp) cc_final: 0.8804 (mtp) REVERT: B 518 ILE cc_start: 0.9398 (mm) cc_final: 0.9058 (tp) REVERT: B 550 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 552 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7732 (m) REVERT: C 171 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: C 297 MET cc_start: 0.8856 (ttm) cc_final: 0.8502 (mtp) REVERT: C 474 MET cc_start: 0.9219 (mmm) cc_final: 0.8925 (mmm) REVERT: C 562 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9111 (mtpp) REVERT: C 596 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8869 (mtmt) REVERT: C 722 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8950 (tp) REVERT: C 760 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6238 (mm) REVERT: D 28 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5750 (pt0) REVERT: D 137 MET cc_start: 0.9092 (mtp) cc_final: 0.8800 (mtp) REVERT: D 502 MET cc_start: 0.6909 (tpp) cc_final: 0.5950 (ttt) REVERT: D 518 ILE cc_start: 0.9409 (mm) cc_final: 0.9065 (tp) REVERT: D 550 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7311 (t80) REVERT: D 552 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7723 (m) outliers start: 72 outliers final: 49 residues processed: 192 average time/residue: 0.3359 time to fit residues: 108.8256 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 : 2.304 ------------------------------------------------------------------------------- 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 562 LYS 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 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 56 TRP 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 550 PHE Chi-restraints excluded: chain B residue 552 VAL 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 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 562 LYS 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 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 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 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 208 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 50 optimal weight: 0.0170 overall best weight: 1.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN C 34 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 = 0.3884 r_free = 0.3884 target = 0.120360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075076 restraints weight = 47430.898| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.51 r_work: 0.2915 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23002 Z= 0.128 Angle : 0.617 16.915 31370 Z= 0.303 Chirality : 0.042 0.384 3528 Planarity : 0.003 0.033 3914 Dihedral : 5.142 59.259 3722 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.01 % Allowed : 18.91 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2700 helix: 1.06 (0.14), residues: 1616 sheet: -1.16 (0.59), residues: 62 loop : -1.73 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 742 HIS 0.008 0.001 HIS D 524 PHE 0.013 0.001 PHE D 549 TYR 0.011 0.001 TYR A 183 ARG 0.004 0.000 ARG D 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 24) link_NAG-ASN : angle 2.11875 ( 72) link_BETA1-4 : bond 0.00359 ( 14) link_BETA1-4 : angle 1.63253 ( 42) hydrogen bonds : bond 0.04038 ( 1083) hydrogen bonds : angle 4.11494 ( 3189) metal coordination : bond 0.00118 ( 4) SS BOND : bond 0.00812 ( 10) SS BOND : angle 4.46548 ( 20) covalent geometry : bond 0.00295 (22948) covalent geometry : angle 0.59674 (31236) Misc. bond : bond 0.00626 ( 2) *********************** 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 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 297 MET cc_start: 0.8882 (ttm) cc_final: 0.8542 (mtp) REVERT: A 474 MET cc_start: 0.9218 (mmm) cc_final: 0.8962 (mmm) REVERT: A 562 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9113 (mtpp) REVERT: A 596 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8869 (mtmt) REVERT: A 722 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8899 (tp) REVERT: A 760 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6255 (mm) REVERT: B 28 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5817 (pt0) REVERT: B 137 MET cc_start: 0.9109 (mtp) cc_final: 0.8869 (mtp) REVERT: B 435 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7249 (m110) REVERT: B 518 ILE cc_start: 0.9395 (mm) cc_final: 0.9070 (tp) REVERT: B 550 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7212 (t80) REVERT: B 552 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7692 (m) REVERT: C 171 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: C 297 MET cc_start: 0.8849 (ttm) cc_final: 0.8497 (mtp) REVERT: C 474 MET cc_start: 0.9211 (mmm) cc_final: 0.8960 (mmm) REVERT: C 562 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9108 (mtpp) REVERT: C 596 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8893 (mtmt) REVERT: C 722 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8904 (tp) REVERT: C 760 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6238 (mm) REVERT: D 28 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5815 (pt0) REVERT: D 137 MET cc_start: 0.9128 (mtp) cc_final: 0.8891 (mtp) REVERT: D 435 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7116 (m110) REVERT: D 439 VAL cc_start: 0.8333 (t) cc_final: 0.8103 (p) REVERT: D 550 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7355 (t80) REVERT: D 552 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7707 (m) outliers start: 72 outliers final: 46 residues processed: 192 average time/residue: 0.3081 time to fit residues: 99.8885 Evaluate side-chains 184 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 120 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 562 LYS 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 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 56 TRP 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 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 B residue 552 VAL 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 351 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 562 LYS 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 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 550 PHE Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 573 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 152 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075251 restraints weight = 46262.325| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.51 r_work: 0.2907 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23002 Z= 0.134 Angle : 0.619 16.531 31370 Z= 0.304 Chirality : 0.043 0.306 3528 Planarity : 0.004 0.032 3914 Dihedral : 5.019 58.826 3722 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.97 % Allowed : 18.87 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2700 helix: 1.14 (0.14), residues: 1614 sheet: -1.25 (0.56), residues: 66 loop : -1.70 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 742 HIS 0.004 0.001 HIS B 296 PHE 0.026 0.001 PHE D 548 TYR 0.012 0.001 TYR A 183 ARG 0.002 0.000 ARG D 14 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 24) link_NAG-ASN : angle 2.06902 ( 72) link_BETA1-4 : bond 0.00356 ( 14) link_BETA1-4 : angle 1.59681 ( 42) hydrogen bonds : bond 0.04089 ( 1083) hydrogen bonds : angle 4.09451 ( 3189) metal coordination : bond 0.00166 ( 4) SS BOND : bond 0.00797 ( 10) SS BOND : angle 4.42085 ( 20) covalent geometry : bond 0.00315 (22948) covalent geometry : angle 0.59915 (31236) Misc. bond : bond 0.00465 ( 2) *********************** 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 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 124 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: A 297 MET cc_start: 0.8868 (ttm) cc_final: 0.8514 (mtp) REVERT: A 474 MET cc_start: 0.9233 (mmm) cc_final: 0.8936 (mmm) REVERT: A 562 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9104 (mtpp) REVERT: A 596 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8869 (mtmt) REVERT: A 722 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8930 (tp) REVERT: A 760 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6259 (mm) REVERT: B 28 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5814 (pt0) REVERT: B 137 MET cc_start: 0.9105 (mtp) cc_final: 0.8882 (mtp) REVERT: B 518 ILE cc_start: 0.9394 (mm) cc_final: 0.9073 (tp) REVERT: B 550 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7272 (t80) REVERT: B 552 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7708 (m) REVERT: C 171 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: C 297 MET cc_start: 0.8864 (ttm) cc_final: 0.8514 (mtp) REVERT: C 474 MET cc_start: 0.9239 (mmm) cc_final: 0.8939 (mmm) REVERT: C 562 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9103 (mtpp) REVERT: C 596 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (mtmt) REVERT: C 722 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8934 (tp) REVERT: C 760 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6242 (mm) REVERT: D 28 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5828 (pt0) REVERT: D 137 MET cc_start: 0.9109 (mtp) cc_final: 0.8883 (mtp) REVERT: D 550 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7365 (t80) REVERT: D 552 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7707 (m) outliers start: 71 outliers final: 48 residues processed: 189 average time/residue: 0.3011 time to fit residues: 96.4705 Evaluate side-chains 188 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 2.639 ------------------------------------------------------------------------------- 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 463 VAL Chi-restraints excluded: chain A residue 562 LYS 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 752 VAL 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 56 TRP 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 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 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 562 LYS 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 D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 187 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 229 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN C 34 HIS D 435 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.120830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075391 restraints weight = 46715.948| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.60 r_work: 0.2914 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23002 Z= 0.120 Angle : 0.604 15.280 31370 Z= 0.297 Chirality : 0.042 0.322 3528 Planarity : 0.003 0.033 3914 Dihedral : 4.855 58.050 3722 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.64 % Allowed : 19.58 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2700 helix: 1.21 (0.14), residues: 1624 sheet: -1.17 (0.55), residues: 66 loop : -1.63 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 742 HIS 0.004 0.001 HIS C 34 PHE 0.022 0.001 PHE D 548 TYR 0.010 0.001 TYR C 183 ARG 0.002 0.000 ARG B 14 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 24) link_NAG-ASN : angle 2.00361 ( 72) link_BETA1-4 : bond 0.00377 ( 14) link_BETA1-4 : angle 1.55334 ( 42) hydrogen bonds : bond 0.03862 ( 1083) hydrogen bonds : angle 4.04821 ( 3189) metal coordination : bond 0.00120 ( 4) SS BOND : bond 0.00644 ( 10) SS BOND : angle 4.75050 ( 20) covalent geometry : bond 0.00276 (22948) covalent geometry : angle 0.58215 (31236) Misc. bond : bond 0.00395 ( 2) ********************** 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 191 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8669 (pmm) cc_final: 0.8170 (pmm) REVERT: A 171 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 297 MET cc_start: 0.8920 (ttm) cc_final: 0.8584 (mtp) REVERT: A 474 MET cc_start: 0.9225 (mmm) cc_final: 0.9011 (mmm) REVERT: A 562 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9128 (mtpp) REVERT: A 596 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8870 (mtmt) REVERT: A 722 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8913 (tp) REVERT: A 760 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6319 (mm) REVERT: B 28 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5810 (pt0) REVERT: B 550 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7349 (t80) REVERT: B 552 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7741 (m) REVERT: C 82 MET cc_start: 0.8681 (pmm) cc_final: 0.8156 (pmm) REVERT: C 171 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 297 MET cc_start: 0.8922 (ttm) cc_final: 0.8581 (mtp) REVERT: C 562 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9118 (mtpp) REVERT: C 596 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8883 (mtmt) REVERT: C 760 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6311 (mm) REVERT: D 28 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5729 (pt0) REVERT: D 455 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5656 (pttp) REVERT: D 550 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7426 (t80) REVERT: D 552 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7744 (m) outliers start: 63 outliers final: 43 residues processed: 183 average time/residue: 0.3085 time to fit residues: 94.4071 Evaluate side-chains 180 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 562 LYS 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 752 VAL 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 56 TRP 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 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 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 34 HIS 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 562 LYS 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 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 56 TRP Chi-restraints excluded: chain D residue 92 ILE 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 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 264 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 246 optimal weight: 0.0970 chunk 208 optimal weight: 0.0170 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3896 r_free = 0.3896 target = 0.121507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076307 restraints weight = 46372.499| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.58 r_work: 0.2933 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23002 Z= 0.104 Angle : 0.586 14.505 31370 Z= 0.287 Chirality : 0.041 0.280 3528 Planarity : 0.003 0.032 3914 Dihedral : 4.708 57.191 3722 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.43 % Allowed : 19.87 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2700 helix: 1.24 (0.14), residues: 1636 sheet: -1.06 (0.56), residues: 66 loop : -1.59 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 742 HIS 0.019 0.001 HIS C 34 PHE 0.020 0.001 PHE D 548 TYR 0.008 0.001 TYR A 183 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 24) link_NAG-ASN : angle 1.96844 ( 72) link_BETA1-4 : bond 0.00373 ( 14) link_BETA1-4 : angle 1.51639 ( 42) hydrogen bonds : bond 0.03707 ( 1083) hydrogen bonds : angle 4.00079 ( 3189) metal coordination : bond 0.00064 ( 4) SS BOND : bond 0.00560 ( 10) SS BOND : angle 4.55116 ( 20) covalent geometry : bond 0.00229 (22948) covalent geometry : angle 0.56580 (31236) Misc. bond : bond 0.00376 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15914.77 seconds wall clock time: 277 minutes 53.43 seconds (16673.43 seconds total)