Starting phenix.real_space_refine on Thu May 22 02:43:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.map" model { file = "/net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i93_35256/05_2025/8i93_35256.cif" } resolution = 3.1 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 130 5.16 5 C 14476 2.51 5 N 3566 2.21 5 O 4168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22342 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 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: 12.15, per 1000 atoms: 0.54 Number of scatterers: 22342 At special positions: 0 Unit cell: (111.961, 135.875, 182.616, 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 130 16.00 O 4168 8.00 N 3566 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 " Time building additional restraints: 7.35 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 378 " pdb=" ZN C 902 " 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: 130 helices and 10 sheets defined 63.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 52 removed outlier: 3.914A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.170A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 4.115A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.680A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.670A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.558A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.883A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.745A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.508A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.605A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.815A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.871A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.793A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.095A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.751A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.990A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.531A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.801A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.749A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.955A pdb=" N LYS A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 767 removed outlier: 3.758A pdb=" N GLY A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 26 through 30 removed outlier: 4.111A pdb=" N SER B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.774A pdb=" N TYR B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B 49 " --> pdb=" O CYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 71 through 96 removed outlier: 5.134A pdb=" N ILE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.686A pdb=" N LYS B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.995A pdb=" N MET B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.086A pdb=" N ASP B 152 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.580A pdb=" N TRP B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.564A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 4.436A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 4.548A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.758A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.881A 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 298 through 314 removed outlier: 3.871A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 349 removed outlier: 3.715A pdb=" N ALA B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.272A pdb=" N ASN B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 355 " --> pdb=" O GLU B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.531A pdb=" N ASN B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.697A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 445 removed outlier: 3.534A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 454 through 470 removed outlier: 4.198A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 508 Proline residue: B 493 - end of helix removed outlier: 3.774A pdb=" N ILE B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.775A pdb=" N PHE B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.525A pdb=" N GLN B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 581 through 591 removed outlier: 4.229A pdb=" N VAL B 585 " --> pdb=" O TRP B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 6.232A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.584A pdb=" N ASN B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 52 removed outlier: 3.913A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 4.171A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 4.115A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.679A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.670A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 removed outlier: 3.558A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.884A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.745A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.508A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.605A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 383 removed outlier: 3.814A pdb=" N THR C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.870A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 removed outlier: 3.793A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 4.095A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 Processing helix chain 'C' and resid 449 through 464 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.752A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 526 " --> pdb=" O GLN C 522 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.991A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.530A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.801A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.749A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.955A pdb=" N LYS C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 removed outlier: 3.758A pdb=" N GLY C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 765 " --> pdb=" O ILE C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 30 removed outlier: 4.112A pdb=" N SER D 30 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.775A pdb=" N TYR D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS D 49 " --> pdb=" O CYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 71 through 96 removed outlier: 5.134A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.685A pdb=" N LYS D 112 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.995A pdb=" N MET D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 148 through 152 removed outlier: 4.086A pdb=" N ASP D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.580A pdb=" N TRP D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.564A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 209 " --> pdb=" O TRP D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 4.436A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.549A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.758A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 3.882A 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 298 through 314 removed outlier: 3.871A pdb=" N ASP D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 349 removed outlier: 3.716A pdb=" N ALA D 318 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.273A pdb=" N ASN D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL D 355 " --> pdb=" O GLU D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 355' Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.531A pdb=" N ASN D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.696A pdb=" N ALA D 376 " --> pdb=" O PRO D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 445 removed outlier: 3.534A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 418 " --> pdb=" O PRO D 414 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D 430 " --> pdb=" O CYS D 426 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET D 432 " --> pdb=" O GLY D 428 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 454 through 470 removed outlier: 4.197A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 508 Proline residue: D 493 - end of helix removed outlier: 3.774A pdb=" N ILE D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.775A pdb=" N PHE D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.526A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 581 through 591 removed outlier: 4.230A pdb=" N VAL D 585 " --> pdb=" O TRP D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 608 removed outlier: 6.232A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 3.584A pdb=" N ASN D 608 " --> pdb=" O LYS D 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.884A 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: 6.380A 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 559 through 562 removed outlier: 4.148A pdb=" N GLN B 574 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.884A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.380A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'D' and resid 559 through 562 removed outlier: 4.148A pdb=" N GLN D 574 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6727 1.33 - 1.46: 6245 1.46 - 1.59: 9760 1.59 - 1.72: 0 1.72 - 1.84: 214 Bond restraints: 22946 Sorted by residual: bond pdb=" C ASN A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.337 1.292 0.045 9.80e-03 1.04e+04 2.08e+01 bond pdb=" C ASN C 137 " pdb=" N PRO C 138 " ideal model delta sigma weight residual 1.337 1.293 0.044 9.80e-03 1.04e+04 2.01e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" CB TRP A 461 " pdb=" CG TRP A 461 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.11e+00 bond pdb=" CB TRP C 461 " pdb=" CG TRP C 461 " ideal model delta sigma weight residual 1.498 1.422 0.076 3.10e-02 1.04e+03 6.08e+00 ... (remaining 22941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 30193 2.41 - 4.82: 923 4.82 - 7.23: 102 7.23 - 9.64: 12 9.64 - 12.05: 2 Bond angle restraints: 31232 Sorted by residual: angle pdb=" N GLU B 352 " pdb=" CA GLU B 352 " pdb=" C GLU B 352 " ideal model delta sigma weight residual 111.14 118.60 -7.46 1.08e+00 8.57e-01 4.78e+01 angle pdb=" N GLU D 352 " pdb=" CA GLU D 352 " pdb=" C GLU D 352 " ideal model delta sigma weight residual 111.14 118.58 -7.44 1.08e+00 8.57e-01 4.75e+01 angle pdb=" N ILE D 309 " pdb=" CA ILE D 309 " pdb=" C ILE D 309 " ideal model delta sigma weight residual 113.42 107.21 6.21 1.17e+00 7.31e-01 2.82e+01 angle pdb=" N ILE B 309 " pdb=" CA ILE B 309 " pdb=" C ILE B 309 " ideal model delta sigma weight residual 113.42 107.28 6.14 1.17e+00 7.31e-01 2.76e+01 angle pdb=" N LEU C 656 " pdb=" CA LEU C 656 " pdb=" C LEU C 656 " ideal model delta sigma weight residual 114.62 108.94 5.68 1.14e+00 7.69e-01 2.48e+01 ... (remaining 31227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 12045 17.34 - 34.68: 1348 34.68 - 52.02: 431 52.02 - 69.36: 78 69.36 - 86.70: 46 Dihedral angle restraints: 13948 sinusoidal: 6038 harmonic: 7910 Sorted by residual: dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA CYS C 344 " pdb=" C CYS C 344 " pdb=" N HIS C 345 " pdb=" CA HIS C 345 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA TYR D 174 " pdb=" C TYR D 174 " pdb=" N PHE D 175 " pdb=" CA PHE D 175 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 13945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2274 0.055 - 0.110: 1062 0.110 - 0.164: 157 0.164 - 0.219: 27 0.219 - 0.274: 8 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 463 " pdb=" CA VAL C 463 " pdb=" CG1 VAL C 463 " pdb=" CG2 VAL C 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU D 352 " pdb=" N GLU D 352 " pdb=" C GLU D 352 " pdb=" CB GLU D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3525 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " 0.051 2.00e-02 2.50e+03 5.37e-02 3.60e+01 pdb=" CG ASN D 258 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 258 " 0.051 2.00e-02 2.50e+03 5.36e-02 3.59e+01 pdb=" CG ASN B 258 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 258 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 258 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 676 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 677 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " -0.033 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 166 2.51 - 3.11: 17823 3.11 - 3.71: 32692 3.71 - 4.30: 47201 4.30 - 4.90: 78498 Nonbonded interactions: 176380 Sorted by model distance: nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.913 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.913 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.021 2.230 nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.021 2.230 nonbonded pdb=" CE1 HIS C 374 " pdb="ZN ZN C 902 " model vdw 2.109 2.450 ... (remaining 176375 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: 0.04 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.260 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.015 0.578 22996 Z= 0.653 Angle : 0.998 12.483 31366 Z= 0.549 Chirality : 0.060 0.274 3528 Planarity : 0.005 0.062 3912 Dihedral : 16.714 86.699 8830 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.56 % Favored : 89.37 % Rotamer: Outliers : 3.93 % Allowed : 13.31 % Favored : 82.76 % 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: -3.81 (0.13), residues: 2700 helix: -1.91 (0.11), residues: 1568 sheet: -1.21 (0.72), residues: 42 loop : -3.47 (0.15), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 566 HIS 0.007 0.002 HIS C 241 PHE 0.035 0.002 PHE B 48 TYR 0.027 0.002 TYR C 385 ARG 0.005 0.001 ARG C 161 Details of bonding type rmsd link_NAG-ASN : bond 0.04271 ( 24) link_NAG-ASN : angle 4.36462 ( 72) link_BETA1-4 : bond 0.01187 ( 14) link_BETA1-4 : angle 2.85543 ( 42) hydrogen bonds : bond 0.15763 ( 1048) hydrogen bonds : angle 6.55706 ( 3090) metal coordination : bond 0.57746 ( 2) SS BOND : bond 0.00247 ( 10) SS BOND : angle 2.30645 ( 20) covalent geometry : bond 0.01436 (22946) covalent geometry : angle 0.97026 (31232) *********************** 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 437 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 343 time to evaluate : 2.282 Fit side-chains outliers start: 94 outliers final: 36 residues processed: 423 average time/residue: 0.2873 time to fit residues: 198.1612 Evaluate side-chains 188 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain D residue 701 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 210 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 ASN A 117 ASN A 149 ASN A 159 ASN A 175 GLN A 239 HIS A 305 GLN A 340 GLN A 345 HIS A 374 HIS A 378 HIS A 401 HIS A 437 ASN A 493 HIS A 505 HIS A 522 GLN A 586 ASN A 601 ASN B 8 ASN B 63 GLN B 142 ASN B 340 ASN B 365 GLN B 435 ASN C 58 ASN C 63 ASN C 117 ASN C 149 ASN C 159 ASN C 175 GLN C 239 HIS C 305 GLN C 340 GLN C 345 HIS C 374 HIS C 378 HIS C 401 HIS C 437 ASN C 493 HIS C 505 HIS C 522 GLN C 586 ASN C 601 ASN D 8 ASN D 63 GLN D 130 ASN D 142 ASN D 340 ASN D 365 GLN D 435 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.125370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079747 restraints weight = 44675.586| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.77 r_work: 0.2903 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.638 22996 Z= 0.248 Angle : 0.680 8.732 31366 Z= 0.347 Chirality : 0.044 0.206 3528 Planarity : 0.005 0.042 3912 Dihedral : 8.001 59.821 3773 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.76 % Allowed : 15.90 % Favored : 81.34 % 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: -2.27 (0.15), residues: 2700 helix: -0.70 (0.13), residues: 1602 sheet: -1.10 (0.70), residues: 42 loop : -2.78 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 196 HIS 0.004 0.001 HIS C 378 PHE 0.022 0.002 PHE D 529 TYR 0.018 0.002 TYR C 83 ARG 0.004 0.001 ARG C 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 24) link_NAG-ASN : angle 2.27094 ( 72) link_BETA1-4 : bond 0.00381 ( 14) link_BETA1-4 : angle 2.03545 ( 42) hydrogen bonds : bond 0.05421 ( 1048) hydrogen bonds : angle 4.69553 ( 3090) metal coordination : bond 0.63744 ( 2) SS BOND : bond 0.00227 ( 10) SS BOND : angle 1.68123 ( 20) covalent geometry : bond 0.00326 (22946) covalent geometry : angle 0.66699 (31232) *********************** 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 256 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 2.259 Fit side-chains REVERT: A 62 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7472 (ptm) REVERT: A 661 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: A 722 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9101 (tt) REVERT: A 723 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: B 209 TYR cc_start: 0.6660 (t80) cc_final: 0.6200 (t80) REVERT: B 270 ASP cc_start: 0.8733 (m-30) cc_final: 0.8383 (m-30) REVERT: B 542 MET cc_start: 0.8301 (mmm) cc_final: 0.7991 (mmt) REVERT: B 553 GLU cc_start: 0.6117 (tm-30) cc_final: 0.5769 (pm20) REVERT: C 62 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: C 190 MET cc_start: 0.8842 (tmm) cc_final: 0.8626 (tmm) REVERT: C 476 LYS cc_start: 0.9356 (mptt) cc_final: 0.9130 (mmmm) REVERT: C 661 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: C 722 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9090 (tt) REVERT: C 723 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8762 (pt0) REVERT: D 209 TYR cc_start: 0.6687 (t80) cc_final: 0.6109 (t80) REVERT: D 270 ASP cc_start: 0.8742 (m-30) cc_final: 0.8392 (m-30) REVERT: D 542 MET cc_start: 0.8320 (mmm) cc_final: 0.8022 (mmt) REVERT: D 544 ILE cc_start: 0.7625 (mm) cc_final: 0.7359 (tt) REVERT: D 546 PHE cc_start: 0.7822 (t80) cc_final: 0.7534 (t80) REVERT: D 553 GLU cc_start: 0.6048 (tm-30) cc_final: 0.5755 (pm20) REVERT: B 701 MET cc_start: 0.6758 (mpt) cc_final: 0.5499 (mpt) REVERT: D 701 MET cc_start: 0.6795 (mpt) cc_final: 0.5516 (mpt) outliers start: 66 outliers final: 29 residues processed: 247 average time/residue: 0.3168 time to fit residues: 130.0584 Evaluate side-chains 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.125614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080236 restraints weight = 44811.997| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.78 r_work: 0.2915 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22996 Z= 0.124 Angle : 0.595 8.055 31366 Z= 0.300 Chirality : 0.042 0.193 3528 Planarity : 0.004 0.035 3912 Dihedral : 6.625 59.173 3733 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 2.59 % Allowed : 16.69 % Favored : 80.71 % 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: -1.51 (0.16), residues: 2700 helix: -0.08 (0.13), residues: 1612 sheet: -1.41 (0.69), residues: 42 loop : -2.46 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.006 0.001 HIS A 378 PHE 0.018 0.001 PHE D 48 TYR 0.010 0.001 TYR C 516 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 24) link_NAG-ASN : angle 1.99821 ( 72) link_BETA1-4 : bond 0.00332 ( 14) link_BETA1-4 : angle 1.89737 ( 42) hydrogen bonds : bond 0.04430 ( 1048) hydrogen bonds : angle 4.29346 ( 3090) metal coordination : bond 0.01250 ( 2) SS BOND : bond 0.00895 ( 10) SS BOND : angle 1.55779 ( 20) covalent geometry : bond 0.00273 (22946) covalent geometry : angle 0.58285 (31232) *********************** 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 247 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 2.441 Fit side-chains REVERT: A 476 LYS cc_start: 0.9341 (mptt) cc_final: 0.9135 (mmmm) REVERT: A 661 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: A 723 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8768 (pt0) REVERT: B 89 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7785 (mt-10) REVERT: B 209 TYR cc_start: 0.6642 (t80) cc_final: 0.6361 (t80) REVERT: B 270 ASP cc_start: 0.8595 (m-30) cc_final: 0.8222 (m-30) REVERT: B 542 MET cc_start: 0.8527 (mmm) cc_final: 0.8310 (mmt) REVERT: B 553 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6125 (pm20) REVERT: C 190 MET cc_start: 0.8811 (tmm) cc_final: 0.8569 (tmm) REVERT: C 476 LYS cc_start: 0.9339 (mptt) cc_final: 0.9128 (mmmm) REVERT: C 661 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: D 209 TYR cc_start: 0.6863 (t80) cc_final: 0.6640 (t80) REVERT: D 210 MET cc_start: 0.7942 (tmm) cc_final: 0.7511 (tmm) REVERT: D 270 ASP cc_start: 0.8584 (m-30) cc_final: 0.8200 (m-30) REVERT: D 542 MET cc_start: 0.8520 (mmm) cc_final: 0.8314 (mmt) REVERT: D 544 ILE cc_start: 0.7662 (mm) cc_final: 0.7356 (tt) REVERT: D 553 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6114 (pm20) outliers start: 62 outliers final: 37 residues processed: 232 average time/residue: 0.2837 time to fit residues: 110.9778 Evaluate side-chains 202 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 527 ASN D 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075269 restraints weight = 44860.830| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.50 r_work: 0.2855 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22996 Z= 0.217 Angle : 0.656 9.699 31366 Z= 0.329 Chirality : 0.045 0.244 3528 Planarity : 0.004 0.039 3912 Dihedral : 6.266 58.250 3729 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 3.26 % Allowed : 17.53 % Favored : 79.21 % 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: -1.29 (0.16), residues: 2700 helix: 0.08 (0.13), residues: 1612 sheet: -1.14 (0.72), residues: 42 loop : -2.34 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 195 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE C 464 TYR 0.015 0.002 TYR A 385 ARG 0.005 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 24) link_NAG-ASN : angle 2.22134 ( 72) link_BETA1-4 : bond 0.00340 ( 14) link_BETA1-4 : angle 1.87161 ( 42) hydrogen bonds : bond 0.05184 ( 1048) hydrogen bonds : angle 4.32208 ( 3090) metal coordination : bond 0.00687 ( 2) SS BOND : bond 0.01413 ( 10) SS BOND : angle 1.82584 ( 20) covalent geometry : bond 0.00515 (22946) covalent geometry : angle 0.64305 (31232) *********************** 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 236 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 158 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.9608 (OUTLIER) cc_final: 0.8762 (t-90) REVERT: A 661 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8729 (mt0) REVERT: A 723 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8885 (pt0) REVERT: B 89 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7963 (mt-10) REVERT: B 224 TYR cc_start: 0.7513 (m-10) cc_final: 0.7228 (m-10) REVERT: B 270 ASP cc_start: 0.8531 (m-30) cc_final: 0.8121 (m-30) REVERT: C 190 MET cc_start: 0.8866 (tmm) cc_final: 0.8554 (tmm) REVERT: C 401 HIS cc_start: 0.9616 (OUTLIER) cc_final: 0.8782 (t-90) REVERT: C 661 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: C 723 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8818 (pt0) REVERT: D 209 TYR cc_start: 0.7026 (t80) cc_final: 0.6803 (t80) REVERT: D 224 TYR cc_start: 0.7439 (m-10) cc_final: 0.7140 (m-10) REVERT: D 270 ASP cc_start: 0.8530 (m-30) cc_final: 0.8138 (m-30) REVERT: D 544 ILE cc_start: 0.7849 (mm) cc_final: 0.7512 (tt) REVERT: B 701 MET cc_start: 0.6733 (mmt) cc_final: 0.6194 (mmm) outliers start: 78 outliers final: 46 residues processed: 226 average time/residue: 0.2849 time to fit residues: 108.7222 Evaluate side-chains 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 198 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.0270 chunk 134 optimal weight: 10.0000 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN D 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.124433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077601 restraints weight = 44853.020| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.55 r_work: 0.2914 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22996 Z= 0.114 Angle : 0.565 8.142 31366 Z= 0.283 Chirality : 0.041 0.197 3528 Planarity : 0.004 0.040 3912 Dihedral : 5.612 59.314 3725 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.38 % Allowed : 17.91 % Favored : 79.71 % 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: -0.83 (0.16), residues: 2700 helix: 0.44 (0.13), residues: 1610 sheet: -1.39 (0.71), residues: 42 loop : -2.10 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 PHE 0.014 0.001 PHE B 546 TYR 0.012 0.001 TYR B 209 ARG 0.008 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 24) link_NAG-ASN : angle 1.90064 ( 72) link_BETA1-4 : bond 0.00305 ( 14) link_BETA1-4 : angle 1.68367 ( 42) hydrogen bonds : bond 0.04044 ( 1048) hydrogen bonds : angle 4.12514 ( 3090) metal coordination : bond 0.00072 ( 2) SS BOND : bond 0.00441 ( 10) SS BOND : angle 1.50685 ( 20) covalent geometry : bond 0.00250 (22946) covalent geometry : angle 0.55445 (31232) *********************** 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 223 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 699 GLU cc_start: 0.8655 (mp0) cc_final: 0.8443 (mp0) REVERT: A 723 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8728 (pt0) REVERT: B 89 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7888 (mt-10) REVERT: B 209 TYR cc_start: 0.6866 (t80) cc_final: 0.6659 (t80) REVERT: B 210 MET cc_start: 0.8129 (tmm) cc_final: 0.7740 (tmm) REVERT: B 224 TYR cc_start: 0.7313 (m-10) cc_final: 0.7061 (m-10) REVERT: B 270 ASP cc_start: 0.8506 (m-30) cc_final: 0.8143 (m-30) REVERT: C 190 MET cc_start: 0.8832 (tmm) cc_final: 0.8497 (tmm) REVERT: C 723 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8675 (pt0) REVERT: D 89 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7895 (mt-10) REVERT: D 209 TYR cc_start: 0.7122 (t80) cc_final: 0.6894 (t80) REVERT: D 210 MET cc_start: 0.8281 (tmm) cc_final: 0.7975 (tmm) REVERT: D 224 TYR cc_start: 0.7356 (m-10) cc_final: 0.7086 (m-10) REVERT: D 270 ASP cc_start: 0.8572 (m-30) cc_final: 0.8119 (m-30) REVERT: D 544 ILE cc_start: 0.7889 (mm) cc_final: 0.7576 (tt) outliers start: 57 outliers final: 34 residues processed: 212 average time/residue: 0.2765 time to fit residues: 98.9881 Evaluate side-chains 188 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 201 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 222 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075946 restraints weight = 44402.659| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.46 r_work: 0.2874 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22996 Z= 0.166 Angle : 0.595 9.045 31366 Z= 0.297 Chirality : 0.043 0.248 3528 Planarity : 0.004 0.040 3912 Dihedral : 5.346 59.384 3721 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 2.80 % Allowed : 17.78 % Favored : 79.41 % 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: -0.70 (0.16), residues: 2700 helix: 0.54 (0.13), residues: 1610 sheet: -1.44 (0.71), residues: 42 loop : -2.04 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 195 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 464 TYR 0.012 0.001 TYR C 385 ARG 0.007 0.000 ARG C 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 24) link_NAG-ASN : angle 2.04099 ( 72) link_BETA1-4 : bond 0.00310 ( 14) link_BETA1-4 : angle 1.72505 ( 42) hydrogen bonds : bond 0.04564 ( 1048) hydrogen bonds : angle 4.12371 ( 3090) metal coordination : bond 0.00224 ( 2) SS BOND : bond 0.00617 ( 10) SS BOND : angle 1.59703 ( 20) covalent geometry : bond 0.00390 (22946) covalent geometry : angle 0.58341 (31232) *********************** 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 218 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7658 (ttt90) REVERT: A 401 HIS cc_start: 0.9615 (OUTLIER) cc_final: 0.8860 (t-90) REVERT: A 699 GLU cc_start: 0.8706 (mp0) cc_final: 0.8436 (mp0) REVERT: A 723 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8811 (pt0) REVERT: B 89 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7947 (mt-10) REVERT: B 209 TYR cc_start: 0.7169 (t80) cc_final: 0.6900 (t80) REVERT: B 210 MET cc_start: 0.8271 (tmm) cc_final: 0.7978 (tmm) REVERT: B 224 TYR cc_start: 0.7290 (m-10) cc_final: 0.7050 (m-10) REVERT: B 270 ASP cc_start: 0.8493 (m-30) cc_final: 0.8131 (m-30) REVERT: C 115 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7648 (ttt90) REVERT: C 190 MET cc_start: 0.8859 (tmm) cc_final: 0.8542 (tmm) REVERT: C 363 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7930 (mmtt) REVERT: C 401 HIS cc_start: 0.9622 (OUTLIER) cc_final: 0.8870 (t-90) REVERT: C 723 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8752 (pt0) REVERT: D 87 TYR cc_start: 0.6637 (t80) cc_final: 0.6420 (t80) REVERT: D 89 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8035 (mt-10) REVERT: D 209 TYR cc_start: 0.7225 (t80) cc_final: 0.6933 (t80) REVERT: D 210 MET cc_start: 0.8343 (tmm) cc_final: 0.7982 (tmm) REVERT: D 224 TYR cc_start: 0.7282 (m-10) cc_final: 0.7034 (m-10) REVERT: D 270 ASP cc_start: 0.8541 (m-30) cc_final: 0.8131 (m-30) REVERT: D 544 ILE cc_start: 0.8031 (mm) cc_final: 0.7723 (tt) outliers start: 67 outliers final: 44 residues processed: 209 average time/residue: 0.2953 time to fit residues: 102.8124 Evaluate side-chains 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.3980 chunk 267 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.123516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077058 restraints weight = 44485.726| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.47 r_work: 0.2904 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22996 Z= 0.126 Angle : 0.563 9.087 31366 Z= 0.281 Chirality : 0.041 0.218 3528 Planarity : 0.004 0.039 3912 Dihedral : 5.126 59.372 3721 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.68 % Allowed : 18.54 % Favored : 78.79 % 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: -0.48 (0.16), residues: 2700 helix: 0.68 (0.13), residues: 1624 sheet: -1.41 (0.73), residues: 42 loop : -1.92 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE B 546 TYR 0.010 0.001 TYR A 516 ARG 0.007 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 24) link_NAG-ASN : angle 1.89567 ( 72) link_BETA1-4 : bond 0.00308 ( 14) link_BETA1-4 : angle 1.61905 ( 42) hydrogen bonds : bond 0.04061 ( 1048) hydrogen bonds : angle 4.05606 ( 3090) metal coordination : bond 0.00109 ( 2) SS BOND : bond 0.00762 ( 10) SS BOND : angle 1.41469 ( 20) covalent geometry : bond 0.00288 (22946) covalent geometry : angle 0.55204 (31232) *********************** 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 217 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7638 (ttt90) REVERT: A 363 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7951 (mmtt) REVERT: A 579 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8540 (ttm) REVERT: A 699 GLU cc_start: 0.8727 (mp0) cc_final: 0.8448 (mp0) REVERT: A 723 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8807 (pt0) REVERT: B 89 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7966 (mt-10) REVERT: B 209 TYR cc_start: 0.7126 (t80) cc_final: 0.6864 (t80) REVERT: B 210 MET cc_start: 0.8170 (tmm) cc_final: 0.7727 (tmm) REVERT: B 224 TYR cc_start: 0.7288 (m-10) cc_final: 0.7065 (m-10) REVERT: B 270 ASP cc_start: 0.8506 (m-30) cc_final: 0.8139 (m-30) REVERT: B 436 MET cc_start: 0.8325 (mmm) cc_final: 0.7933 (tpt) REVERT: C 115 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7663 (ttt90) REVERT: C 190 MET cc_start: 0.8872 (tmm) cc_final: 0.8569 (tmm) REVERT: C 579 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8620 (ttm) REVERT: C 723 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: D 87 TYR cc_start: 0.6634 (t80) cc_final: 0.6411 (t80) REVERT: D 89 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8018 (mt-10) REVERT: D 209 TYR cc_start: 0.7234 (t80) cc_final: 0.6959 (t80) REVERT: D 210 MET cc_start: 0.8356 (tmm) cc_final: 0.7974 (tmm) REVERT: D 224 TYR cc_start: 0.7299 (m-10) cc_final: 0.7066 (m-10) REVERT: D 270 ASP cc_start: 0.8490 (m-30) cc_final: 0.8142 (m-30) REVERT: D 544 ILE cc_start: 0.8048 (mm) cc_final: 0.7740 (tt) REVERT: B 701 MET cc_start: 0.6616 (mmt) cc_final: 0.6256 (mmt) REVERT: D 701 MET cc_start: 0.6635 (mmt) cc_final: 0.6262 (mmt) outliers start: 64 outliers final: 44 residues processed: 207 average time/residue: 0.2897 time to fit residues: 99.6451 Evaluate side-chains 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 246 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN D 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.123909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077526 restraints weight = 44380.443| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.46 r_work: 0.2916 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22996 Z= 0.121 Angle : 0.555 9.626 31366 Z= 0.278 Chirality : 0.041 0.251 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.824 59.402 3719 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.68 % Allowed : 18.66 % Favored : 78.66 % 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: -0.31 (0.16), residues: 2700 helix: 0.85 (0.13), residues: 1630 sheet: -1.53 (0.72), residues: 42 loop : -1.89 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE D 546 TYR 0.011 0.001 TYR A 516 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 24) link_NAG-ASN : angle 1.84581 ( 72) link_BETA1-4 : bond 0.00293 ( 14) link_BETA1-4 : angle 1.58215 ( 42) hydrogen bonds : bond 0.03929 ( 1048) hydrogen bonds : angle 3.98581 ( 3090) metal coordination : bond 0.00107 ( 2) SS BOND : bond 0.00546 ( 10) SS BOND : angle 1.35004 ( 20) covalent geometry : bond 0.00275 (22946) covalent geometry : angle 0.54528 (31232) *********************** 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 217 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 2.345 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7594 (ttt90) REVERT: A 401 HIS cc_start: 0.9608 (OUTLIER) cc_final: 0.8845 (t-90) REVERT: A 579 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8488 (ttm) REVERT: A 699 GLU cc_start: 0.8793 (mp0) cc_final: 0.8491 (mp0) REVERT: A 723 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: B 89 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7992 (mt-10) REVERT: B 209 TYR cc_start: 0.7151 (t80) cc_final: 0.6936 (t80) REVERT: B 210 MET cc_start: 0.8179 (tmm) cc_final: 0.7860 (tmm) REVERT: B 224 TYR cc_start: 0.7310 (m-10) cc_final: 0.7094 (m-10) REVERT: B 270 ASP cc_start: 0.8493 (m-30) cc_final: 0.8125 (m-30) REVERT: B 436 MET cc_start: 0.8318 (mmm) cc_final: 0.7970 (tpt) REVERT: C 115 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7609 (ttt90) REVERT: C 190 MET cc_start: 0.8843 (tmm) cc_final: 0.8537 (tmm) REVERT: C 363 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7921 (mmtt) REVERT: C 401 HIS cc_start: 0.9610 (OUTLIER) cc_final: 0.8859 (t-90) REVERT: C 579 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8527 (ttm) REVERT: C 722 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8950 (tp) REVERT: C 723 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8681 (pt0) REVERT: D 85 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5974 (mm) REVERT: D 89 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8039 (mt-10) REVERT: D 210 MET cc_start: 0.8388 (tmm) cc_final: 0.8141 (tmm) REVERT: D 224 TYR cc_start: 0.7238 (m-10) cc_final: 0.7015 (m-10) REVERT: D 270 ASP cc_start: 0.8492 (m-30) cc_final: 0.8124 (m-30) REVERT: D 544 ILE cc_start: 0.8090 (mm) cc_final: 0.7782 (tt) REVERT: B 701 MET cc_start: 0.6455 (mmt) cc_final: 0.6120 (mmt) REVERT: D 701 MET cc_start: 0.6445 (mmt) cc_final: 0.6197 (mmt) outliers start: 64 outliers final: 45 residues processed: 211 average time/residue: 0.3036 time to fit residues: 105.3113 Evaluate side-chains 201 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 266 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.123795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077407 restraints weight = 44255.579| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.48 r_work: 0.2903 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 0.039 22996 Z= 0.127 Angle : 0.568 9.909 31366 Z= 0.282 Chirality : 0.041 0.272 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.708 59.597 3719 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.43 % Allowed : 18.83 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.16), residues: 2700 helix: 0.92 (0.13), residues: 1630 sheet: -1.38 (0.75), residues: 42 loop : -1.86 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS C 241 PHE 0.009 0.001 PHE A 684 TYR 0.012 0.001 TYR D 209 ARG 0.007 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 24) link_NAG-ASN : angle 1.83916 ( 72) link_BETA1-4 : bond 0.00311 ( 14) link_BETA1-4 : angle 1.55302 ( 42) hydrogen bonds : bond 0.03946 ( 1048) hydrogen bonds : angle 3.96188 ( 3090) metal coordination : bond 0.00122 ( 2) SS BOND : bond 0.00711 ( 10) SS BOND : angle 1.33974 ( 20) covalent geometry : bond 0.00292 (22946) covalent geometry : angle 0.55881 (31232) *********************** 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 209 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 2.483 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7610 (ttt90) REVERT: A 363 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7847 (mmtt) REVERT: A 401 HIS cc_start: 0.9616 (OUTLIER) cc_final: 0.8849 (t-90) REVERT: A 579 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (ttm) REVERT: A 722 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8918 (tp) REVERT: A 723 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: B 89 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8014 (mt-10) REVERT: B 210 MET cc_start: 0.8258 (tmm) cc_final: 0.7943 (tmm) REVERT: B 224 TYR cc_start: 0.7271 (m-10) cc_final: 0.7065 (m-10) REVERT: B 270 ASP cc_start: 0.8523 (m-30) cc_final: 0.8168 (m-30) REVERT: B 436 MET cc_start: 0.8318 (mmm) cc_final: 0.7969 (tpt) REVERT: B 542 MET cc_start: 0.8282 (mmm) cc_final: 0.8002 (mmt) REVERT: C 115 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7634 (ttt90) REVERT: C 190 MET cc_start: 0.8811 (tmm) cc_final: 0.8506 (tmm) REVERT: C 401 HIS cc_start: 0.9619 (OUTLIER) cc_final: 0.8869 (t-90) REVERT: C 579 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8571 (ttm) REVERT: C 722 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8924 (tp) REVERT: C 723 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: D 85 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.5988 (mm) REVERT: D 89 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8040 (mt-10) REVERT: D 209 TYR cc_start: 0.7205 (t80) cc_final: 0.6959 (t80) REVERT: D 224 TYR cc_start: 0.7248 (m-10) cc_final: 0.7039 (m-10) REVERT: D 270 ASP cc_start: 0.8503 (m-30) cc_final: 0.8161 (m-30) REVERT: D 544 ILE cc_start: 0.8047 (mm) cc_final: 0.7746 (tt) REVERT: B 701 MET cc_start: 0.6330 (mmt) cc_final: 0.6063 (mmt) REVERT: D 701 MET cc_start: 0.6346 (mmt) cc_final: 0.6137 (mmt) outliers start: 58 outliers final: 41 residues processed: 204 average time/residue: 0.2975 time to fit residues: 101.0634 Evaluate side-chains 195 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 554 VAL 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 142 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 217 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.124628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.078515 restraints weight = 44443.961| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.54 r_work: 0.2919 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22996 Z= 0.109 Angle : 0.560 13.131 31366 Z= 0.277 Chirality : 0.041 0.236 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.553 59.217 3719 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.05 % Allowed : 19.41 % Favored : 78.54 % 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: -0.09 (0.16), residues: 2700 helix: 1.03 (0.13), residues: 1628 sheet: -1.61 (0.72), residues: 42 loop : -1.79 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS C 241 PHE 0.009 0.001 PHE A 684 TYR 0.016 0.001 TYR B 209 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 24) link_NAG-ASN : angle 1.75066 ( 72) link_BETA1-4 : bond 0.00333 ( 14) link_BETA1-4 : angle 1.50577 ( 42) hydrogen bonds : bond 0.03699 ( 1048) hydrogen bonds : angle 3.92535 ( 3090) metal coordination : bond 0.00071 ( 2) SS BOND : bond 0.00646 ( 10) SS BOND : angle 1.45915 ( 20) covalent geometry : bond 0.00241 (22946) covalent geometry : angle 0.55099 (31232) ********************** 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 211 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7551 (ttt90) REVERT: A 363 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7953 (mmtt) REVERT: A 579 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: A 722 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 723 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8705 (pt0) REVERT: B 89 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7996 (mt-10) REVERT: B 209 TYR cc_start: 0.7107 (t80) cc_final: 0.6834 (t80) REVERT: B 210 MET cc_start: 0.8248 (tmm) cc_final: 0.7775 (tmm) REVERT: B 224 TYR cc_start: 0.7319 (m-10) cc_final: 0.7106 (m-10) REVERT: B 270 ASP cc_start: 0.8505 (m-30) cc_final: 0.8152 (m-30) REVERT: B 436 MET cc_start: 0.8316 (mmm) cc_final: 0.7982 (tpt) REVERT: C 115 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7559 (ttt90) REVERT: C 190 MET cc_start: 0.8783 (tmm) cc_final: 0.8441 (tmm) REVERT: C 579 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: C 722 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8957 (tp) REVERT: C 723 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: D 89 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8006 (mt-10) REVERT: D 209 TYR cc_start: 0.7217 (t80) cc_final: 0.6969 (t80) REVERT: D 210 MET cc_start: 0.8329 (tmm) cc_final: 0.7995 (tmm) REVERT: D 270 ASP cc_start: 0.8505 (m-30) cc_final: 0.8162 (m-30) REVERT: D 544 ILE cc_start: 0.8070 (mm) cc_final: 0.7755 (tt) REVERT: B 701 MET cc_start: 0.6436 (mmt) cc_final: 0.6154 (mmt) REVERT: D 701 MET cc_start: 0.6362 (mmt) cc_final: 0.6072 (mmt) outliers start: 49 outliers final: 34 residues processed: 209 average time/residue: 0.2875 time to fit residues: 100.4488 Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 554 VAL 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 241 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS C 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.124551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078720 restraints weight = 44132.121| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.45 r_work: 0.2928 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22996 Z= 0.109 Angle : 0.564 11.293 31366 Z= 0.278 Chirality : 0.041 0.280 3528 Planarity : 0.004 0.039 3912 Dihedral : 4.449 59.501 3719 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.88 % Allowed : 19.58 % Favored : 78.54 % 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: -0.02 (0.16), residues: 2700 helix: 1.07 (0.13), residues: 1632 sheet: -1.50 (0.74), residues: 42 loop : -1.77 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 205 HIS 0.003 0.001 HIS C 374 PHE 0.008 0.001 PHE C 684 TYR 0.012 0.001 TYR D 87 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 24) link_NAG-ASN : angle 1.74041 ( 72) link_BETA1-4 : bond 0.00335 ( 14) link_BETA1-4 : angle 1.48420 ( 42) hydrogen bonds : bond 0.03687 ( 1048) hydrogen bonds : angle 3.90061 ( 3090) metal coordination : bond 0.00059 ( 2) SS BOND : bond 0.00585 ( 10) SS BOND : angle 1.32638 ( 20) covalent geometry : bond 0.00243 (22946) covalent geometry : angle 0.55517 (31232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15174.34 seconds wall clock time: 261 minutes 38.99 seconds (15698.99 seconds total)