Starting phenix.real_space_refine on Sat Jul 4 17:02:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_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_35256/07_2026/8i93_35256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.map" model { file = "/net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i93_35256/07_2026/8i93_35256.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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 chiralities: 4 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 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 chiralities: 4 Time building chain proxies: 5.18, per 1000 atoms: 0.23 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 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: 0.64 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: 3.93 Time building geometry restraints manager: 2.57 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: 11359 17.34 - 34.68: 1304 34.68 - 52.02: 371 52.02 - 69.36: 70 69.36 - 86.70: 46 Dihedral angle restraints: 13150 sinusoidal: 5240 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 13147 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 22.910 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 16.832 86.699 8032 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (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 ARG 0.005 0.001 ARG C 161 TYR 0.027 0.002 TYR C 385 PHE 0.035 0.002 PHE B 48 TRP 0.019 0.002 TRP C 566 HIS 0.007 0.002 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01436 / 0.62 (22946) covalent geometry : angle 0.97026 / 0.54 (31232) SS BOND : bond 0.00247 / 0.13 ( 10) SS BOND : angle 2.30645 / 1.37 ( 20) hydrogen bonds : bond 0.15763 / 10.60 ( 1048) hydrogen bonds : angle 6.55706 / 4.67 ( 3090) metal coordination : bond 0.57746 / 28.98 ( 2) link_BETA1-4 : bond 0.01187 / 0.69 ( 14) link_BETA1-4 : angle 2.85543 / 1.81 ( 42) link_NAG-ASN : bond 0.04271 / 2.66 ( 24) link_NAG-ASN : angle 4.36462 / 2.98 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 343 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 36 residues processed: 423 average time/residue: 0.1301 time to fit residues: 90.9894 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 : 0.637 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 142 ASN D 340 ASN D 365 GLN D 435 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.125663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080517 restraints weight = 44953.055| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.69 r_work: 0.2919 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.618 22996 Z= 0.239 Angle : 0.674 8.728 31366 Z= 0.344 Chirality : 0.044 0.196 3528 Planarity : 0.005 0.042 3912 Dihedral : 6.415 59.024 2975 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 2.68 % Allowed : 15.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.15), residues: 2700 helix: -0.71 (0.13), residues: 1602 sheet: -1.13 (0.71), residues: 42 loop : -2.79 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 559 TYR 0.020 0.002 TYR C 83 PHE 0.022 0.002 PHE D 48 TRP 0.014 0.001 TRP B 196 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (22946) covalent geometry : angle 0.66060 / 0.34 (31232) SS BOND : bond 0.00642 / 0.41 ( 10) SS BOND : angle 1.91359 / 1.14 ( 20) hydrogen bonds : bond 0.05509 / 3.62 ( 1048) hydrogen bonds : angle 4.70132 / 3.23 ( 3090) metal coordination : bond 0.61689 / 30.97 ( 2) link_BETA1-4 : bond 0.00402 / 0.27 ( 14) link_BETA1-4 : angle 1.88122 / 1.21 ( 42) link_NAG-ASN : bond 0.00378 / 0.23 ( 24) link_NAG-ASN : angle 2.31820 / 1.61 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7399 (ptm) REVERT: A 661 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: A 722 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9099 (tt) REVERT: A 723 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: B 209 TYR cc_start: 0.6626 (t80) cc_final: 0.6191 (t80) REVERT: B 270 ASP cc_start: 0.8738 (m-30) cc_final: 0.8395 (m-30) REVERT: B 553 GLU cc_start: 0.6124 (tm-30) cc_final: 0.5770 (pm20) REVERT: B 588 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7786 (tt) REVERT: C 62 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7392 (ptm) REVERT: C 190 MET cc_start: 0.8840 (tmm) cc_final: 0.8613 (tmm) REVERT: C 476 LYS cc_start: 0.9353 (mptt) cc_final: 0.9131 (mmmm) REVERT: C 661 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8290 (mp10) REVERT: C 722 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9109 (tt) REVERT: C 723 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8731 (pt0) REVERT: D 209 TYR cc_start: 0.6659 (t80) cc_final: 0.6067 (t80) REVERT: D 270 ASP cc_start: 0.8748 (m-30) cc_final: 0.8399 (m-30) REVERT: D 544 ILE cc_start: 0.7665 (mm) cc_final: 0.7410 (tt) REVERT: D 553 GLU cc_start: 0.6054 (tm-30) cc_final: 0.5744 (pm20) REVERT: D 588 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 701 MET cc_start: 0.6778 (mpt) cc_final: 0.5452 (mpt) REVERT: D 701 MET cc_start: 0.6819 (mpt) cc_final: 0.5468 (mpt) outliers start: 64 outliers final: 30 residues processed: 246 average time/residue: 0.1255 time to fit residues: 51.7769 Evaluate side-chains 206 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 79 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 B residue 588 ILE 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 Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 246 optimal weight: 0.0370 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 527 ASN D 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.125601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080455 restraints weight = 45093.861| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.02 r_work: 0.2890 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2590 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= 0.126 Angle : 0.596 7.374 31366 Z= 0.301 Chirality : 0.042 0.189 3528 Planarity : 0.004 0.035 3912 Dihedral : 5.507 59.224 2935 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.55 % Allowed : 16.90 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.16), residues: 2700 helix: -0.09 (0.13), residues: 1610 sheet: -1.33 (0.70), residues: 42 loop : -2.43 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.010 0.001 TYR C 41 PHE 0.020 0.001 PHE D 48 TRP 0.011 0.001 TRP A 478 HIS 0.016 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22946) covalent geometry : angle 0.58502 / 0.30 (31232) SS BOND : bond 0.00680 / 0.39 ( 10) SS BOND : angle 1.56534 / 0.95 ( 20) hydrogen bonds : bond 0.04459 / 2.94 ( 1048) hydrogen bonds : angle 4.31804 / 2.96 ( 3090) metal coordination : bond 0.01562 / 0.78 ( 2) link_BETA1-4 : bond 0.00381 / 0.24 ( 14) link_BETA1-4 : angle 1.75677 / 1.14 ( 42) link_NAG-ASN : bond 0.00287 / 0.20 ( 24) link_NAG-ASN : angle 1.97424 / 1.41 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.9243 (mptt) cc_final: 0.8982 (mmmm) REVERT: A 661 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: B 89 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7730 (mt-10) REVERT: B 209 TYR cc_start: 0.6674 (t80) cc_final: 0.6409 (t80) REVERT: B 270 ASP cc_start: 0.8603 (m-30) cc_final: 0.8221 (m-30) REVERT: B 542 MET cc_start: 0.7968 (mmt) cc_final: 0.7730 (mmt) REVERT: B 553 GLU cc_start: 0.6427 (tm-30) cc_final: 0.6115 (pm20) REVERT: C 190 MET cc_start: 0.8635 (tmm) cc_final: 0.8378 (tmm) REVERT: C 476 LYS cc_start: 0.9243 (mptt) cc_final: 0.8979 (mmmm) REVERT: C 661 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: C 753 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6281 (tt) REVERT: D 210 MET cc_start: 0.7922 (tmm) cc_final: 0.7489 (tmm) REVERT: D 270 ASP cc_start: 0.8588 (m-30) cc_final: 0.8194 (m-30) REVERT: D 542 MET cc_start: 0.7997 (mmt) cc_final: 0.7745 (mmt) REVERT: D 544 ILE cc_start: 0.7651 (mm) cc_final: 0.7339 (tt) REVERT: D 553 GLU cc_start: 0.6440 (tm-30) cc_final: 0.6115 (pm20) outliers start: 61 outliers final: 36 residues processed: 231 average time/residue: 0.1249 time to fit residues: 48.8421 Evaluate side-chains 199 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 306 VAL 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 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 C residue 753 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 251 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 244 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.125330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080684 restraints weight = 44986.747| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.67 r_work: 0.2923 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2879 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= 0.120 Angle : 0.573 8.211 31366 Z= 0.288 Chirality : 0.041 0.247 3528 Planarity : 0.004 0.039 3912 Dihedral : 5.180 57.865 2931 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 2.38 % Allowed : 18.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2700 helix: 0.22 (0.13), residues: 1614 sheet: -1.46 (0.70), residues: 42 loop : -2.20 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 559 TYR 0.011 0.001 TYR D 209 PHE 0.013 0.001 PHE B 48 TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22946) covalent geometry : angle 0.56279 / 0.29 (31232) SS BOND : bond 0.00603 / 0.35 ( 10) SS BOND : angle 1.57963 / 0.96 ( 20) hydrogen bonds : bond 0.04159 / 2.73 ( 1048) hydrogen bonds : angle 4.16325 / 2.85 ( 3090) metal coordination : bond 0.00542 / 0.27 ( 2) link_BETA1-4 : bond 0.00297 / 0.20 ( 14) link_BETA1-4 : angle 1.61809 / 1.05 ( 42) link_NAG-ASN : bond 0.00264 / 0.18 ( 24) link_NAG-ASN : angle 1.91376 / 1.36 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 0.877 Fit side-chains REVERT: A 476 LYS cc_start: 0.9332 (mptt) cc_final: 0.9104 (mmmm) REVERT: A 579 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8525 (ttm) REVERT: A 661 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8731 (mt0) REVERT: A 699 GLU cc_start: 0.8568 (mp0) cc_final: 0.7975 (mp0) REVERT: A 723 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: B 89 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7759 (mt-10) REVERT: B 206 SER cc_start: 0.7843 (t) cc_final: 0.7604 (p) REVERT: B 224 TYR cc_start: 0.7498 (m-10) cc_final: 0.7172 (m-10) REVERT: B 270 ASP cc_start: 0.8520 (m-30) cc_final: 0.8142 (m-30) REVERT: C 190 MET cc_start: 0.8776 (tmm) cc_final: 0.8474 (tmm) REVERT: C 476 LYS cc_start: 0.9325 (mptt) cc_final: 0.9096 (mmmm) REVERT: C 559 ARG cc_start: 0.9037 (ptt90) cc_final: 0.8640 (ppt90) REVERT: C 661 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8723 (mt0) REVERT: C 699 GLU cc_start: 0.8530 (mp0) cc_final: 0.7959 (mp0) REVERT: C 723 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8741 (pt0) REVERT: D 89 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7633 (mt-10) REVERT: D 209 TYR cc_start: 0.6856 (t80) cc_final: 0.6578 (t80) REVERT: D 210 MET cc_start: 0.8049 (tmm) cc_final: 0.7655 (tmm) REVERT: D 270 ASP cc_start: 0.8532 (m-30) cc_final: 0.8156 (m-30) REVERT: D 544 ILE cc_start: 0.7727 (mm) cc_final: 0.7436 (tt) REVERT: B 701 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6532 (mmp) REVERT: D 701 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6528 (mmp) outliers start: 57 outliers final: 32 residues processed: 217 average time/residue: 0.1214 time to fit residues: 44.5268 Evaluate side-chains 190 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 507 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 579 MET 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 B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 306 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 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 560 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 692 SER 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 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 Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain D residue 701 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 114 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 239 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.124580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079440 restraints weight = 44681.207| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.00 r_work: 0.2878 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22996 Z= 0.138 Angle : 0.573 10.849 31366 Z= 0.286 Chirality : 0.042 0.173 3528 Planarity : 0.004 0.041 3912 Dihedral : 4.669 59.929 2923 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.80 % Allowed : 17.95 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2700 helix: 0.44 (0.13), residues: 1614 sheet: -1.42 (0.72), residues: 42 loop : -2.07 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.011 0.001 TYR C 516 PHE 0.015 0.001 PHE B 546 TRP 0.009 0.001 TRP B 195 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22946) covalent geometry : angle 0.56283 / 0.28 (31232) SS BOND : bond 0.00555 / 0.32 ( 10) SS BOND : angle 1.45735 / 0.88 ( 20) hydrogen bonds : bond 0.04240 / 2.77 ( 1048) hydrogen bonds : angle 4.09374 / 2.81 ( 3090) metal coordination : bond 0.00132 / 0.06 ( 2) link_BETA1-4 : bond 0.00278 / 0.19 ( 14) link_BETA1-4 : angle 1.56311 / 1.02 ( 42) link_NAG-ASN : bond 0.00285 / 0.20 ( 24) link_NAG-ASN : angle 1.90176 / 1.35 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 1.251 Fit side-chains REVERT: A 401 HIS cc_start: 0.9545 (OUTLIER) cc_final: 0.8798 (t-90) REVERT: A 579 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8553 (ttm) REVERT: A 699 GLU cc_start: 0.8686 (mp0) cc_final: 0.8476 (mp0) REVERT: A 719 ASP cc_start: 0.8309 (t0) cc_final: 0.8095 (t0) REVERT: A 723 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: B 87 TYR cc_start: 0.6507 (t80) cc_final: 0.6256 (t80) REVERT: B 89 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7894 (mt-10) REVERT: B 209 TYR cc_start: 0.6856 (t80) cc_final: 0.6508 (t80) REVERT: B 210 MET cc_start: 0.7998 (tmm) cc_final: 0.7587 (tmm) REVERT: B 224 TYR cc_start: 0.7383 (m-10) cc_final: 0.7127 (m-10) REVERT: B 270 ASP cc_start: 0.8548 (m-30) cc_final: 0.8160 (m-30) REVERT: B 436 MET cc_start: 0.8234 (mmm) cc_final: 0.7957 (tpt) REVERT: B 542 MET cc_start: 0.8471 (mmm) cc_final: 0.8174 (mmt) REVERT: C 190 MET cc_start: 0.8829 (tmm) cc_final: 0.8543 (tmm) REVERT: C 401 HIS cc_start: 0.9561 (OUTLIER) cc_final: 0.8812 (t-90) REVERT: C 579 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8658 (ttm) REVERT: C 719 ASP cc_start: 0.8305 (t0) cc_final: 0.8094 (t0) REVERT: C 723 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8793 (pt0) REVERT: D 87 TYR cc_start: 0.6547 (t80) cc_final: 0.6258 (t80) REVERT: D 89 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7769 (mt-10) REVERT: D 210 MET cc_start: 0.8011 (tmm) cc_final: 0.7624 (tmm) REVERT: D 224 TYR cc_start: 0.7368 (m-10) cc_final: 0.7092 (m-10) REVERT: D 270 ASP cc_start: 0.8556 (m-30) cc_final: 0.8170 (m-30) REVERT: D 542 MET cc_start: 0.8435 (mmm) cc_final: 0.8112 (mmt) REVERT: D 544 ILE cc_start: 0.7832 (mm) cc_final: 0.7525 (tt) REVERT: B 701 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6542 (mmp) outliers start: 67 outliers final: 38 residues processed: 225 average time/residue: 0.1285 time to fit residues: 49.1400 Evaluate side-chains 201 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 560 LEU Chi-restraints excluded: chain A residue 579 MET 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 B residue 55 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 545 ILE 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 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 579 MET 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 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 Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 132 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3848 r_free = 0.3848 target = 0.121411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.074147 restraints weight = 45026.622| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.52 r_work: 0.2840 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22996 Z= 0.254 Angle : 0.675 10.812 31366 Z= 0.335 Chirality : 0.046 0.248 3528 Planarity : 0.004 0.041 3912 Dihedral : 4.926 59.191 2923 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer: Outliers : 3.47 % Allowed : 17.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2700 helix: 0.37 (0.13), residues: 1602 sheet: -1.15 (0.74), residues: 42 loop : -2.08 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 559 TYR 0.021 0.002 TYR C 385 PHE 0.016 0.002 PHE A 683 TRP 0.010 0.002 TRP C 163 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (22946) covalent geometry : angle 0.66358 / 0.33 (31232) SS BOND : bond 0.01177 / 0.68 ( 10) SS BOND : angle 2.03908 / 1.24 ( 20) hydrogen bonds : bond 0.05279 / 3.41 ( 1048) hydrogen bonds : angle 4.29154 / 2.93 ( 3090) metal coordination : bond 0.00391 / 0.19 ( 2) link_BETA1-4 : bond 0.00404 / 0.25 ( 14) link_BETA1-4 : angle 1.67754 / 1.09 ( 42) link_NAG-ASN : bond 0.00521 / 0.34 ( 24) link_NAG-ASN : angle 2.21680 / 1.55 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 145 time to evaluate : 0.953 Fit side-chains REVERT: A 115 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7773 (ttt90) REVERT: A 363 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (mmtt) REVERT: A 401 HIS cc_start: 0.9608 (OUTLIER) cc_final: 0.8770 (t-90) REVERT: A 699 GLU cc_start: 0.8769 (mp0) cc_final: 0.8502 (mp0) REVERT: A 719 ASP cc_start: 0.8327 (t0) cc_final: 0.8112 (t0) REVERT: A 723 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8827 (pt0) REVERT: B 20 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: B 89 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7977 (mt-10) REVERT: B 209 TYR cc_start: 0.7154 (t80) cc_final: 0.6774 (t80) REVERT: B 210 MET cc_start: 0.8186 (tmm) cc_final: 0.7749 (tmm) REVERT: B 224 TYR cc_start: 0.7295 (m-10) cc_final: 0.7036 (m-10) REVERT: B 270 ASP cc_start: 0.8538 (m-30) cc_final: 0.8150 (m-30) REVERT: B 436 MET cc_start: 0.8391 (mmm) cc_final: 0.8006 (tpt) REVERT: C 115 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7765 (ttt90) REVERT: C 190 MET cc_start: 0.8890 (tmm) cc_final: 0.8544 (tmm) REVERT: C 401 HIS cc_start: 0.9613 (OUTLIER) cc_final: 0.8783 (t-90) REVERT: C 719 ASP cc_start: 0.8329 (t0) cc_final: 0.8118 (t0) REVERT: C 723 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8829 (pt0) REVERT: D 20 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: D 85 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5948 (mm) REVERT: D 89 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7861 (mt-10) REVERT: D 209 TYR cc_start: 0.7175 (t80) cc_final: 0.6876 (t80) REVERT: D 210 MET cc_start: 0.8186 (tmm) cc_final: 0.7878 (tmm) REVERT: D 224 TYR cc_start: 0.7289 (m-10) cc_final: 0.7020 (m-10) REVERT: D 270 ASP cc_start: 0.8532 (m-30) cc_final: 0.8149 (m-30) REVERT: D 544 ILE cc_start: 0.8012 (mm) cc_final: 0.7688 (tt) REVERT: D 701 MET cc_start: 0.6955 (mmt) cc_final: 0.6419 (mmm) outliers start: 83 outliers final: 49 residues processed: 217 average time/residue: 0.1336 time to fit residues: 48.8083 Evaluate side-chains 197 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 363 LYS 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 506 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 520 LEU 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 20 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 188 SER 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 415 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 545 ILE 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 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 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 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 723 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 42 MET 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 306 VAL 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 457 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 545 ILE 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 266 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN B 94 GLN D 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.124146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077589 restraints weight = 44595.207| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.55 r_work: 0.2905 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3542 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= 0.112 Angle : 0.564 8.805 31366 Z= 0.280 Chirality : 0.041 0.219 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.628 58.044 2922 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.88 % Allowed : 19.12 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2700 helix: 0.70 (0.13), residues: 1612 sheet: -1.35 (0.73), residues: 42 loop : -1.92 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.011 0.001 TYR C 516 PHE 0.011 0.001 PHE D 546 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22946) covalent geometry : angle 0.55434 / 0.28 (31232) SS BOND : bond 0.00770 / 0.45 ( 10) SS BOND : angle 1.46964 / 0.89 ( 20) hydrogen bonds : bond 0.03956 / 2.59 ( 1048) hydrogen bonds : angle 4.08405 / 2.79 ( 3090) metal coordination : bond 0.00024 / 0.01 ( 2) link_BETA1-4 : bond 0.00326 / 0.22 ( 14) link_BETA1-4 : angle 1.46210 / 0.95 ( 42) link_NAG-ASN : bond 0.00265 / 0.18 ( 24) link_NAG-ASN : angle 1.81150 / 1.30 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 401 HIS cc_start: 0.9594 (OUTLIER) cc_final: 0.8809 (t-90) REVERT: A 699 GLU cc_start: 0.8736 (mp0) cc_final: 0.8463 (mp0) REVERT: A 719 ASP cc_start: 0.8227 (t0) cc_final: 0.8000 (t0) REVERT: A 723 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: B 89 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7905 (mt-10) REVERT: B 209 TYR cc_start: 0.7142 (t80) cc_final: 0.6841 (t80) REVERT: B 210 MET cc_start: 0.8138 (tmm) cc_final: 0.7716 (tmm) REVERT: B 224 TYR cc_start: 0.7304 (m-10) cc_final: 0.7085 (m-10) REVERT: B 270 ASP cc_start: 0.8493 (m-30) cc_final: 0.8129 (m-30) REVERT: B 436 MET cc_start: 0.8315 (mmm) cc_final: 0.7934 (tpt) REVERT: C 190 MET cc_start: 0.8829 (tmm) cc_final: 0.8529 (tmm) REVERT: C 401 HIS cc_start: 0.9599 (OUTLIER) cc_final: 0.8814 (t-90) REVERT: C 719 ASP cc_start: 0.8227 (t0) cc_final: 0.8003 (t0) REVERT: C 723 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8701 (pt0) REVERT: D 85 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5988 (mm) REVERT: D 87 TYR cc_start: 0.6523 (t80) cc_final: 0.6268 (t80) REVERT: D 89 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7791 (mt-10) REVERT: D 209 TYR cc_start: 0.7147 (t80) cc_final: 0.6891 (t80) REVERT: D 210 MET cc_start: 0.8138 (tmm) cc_final: 0.7860 (tmm) REVERT: D 224 TYR cc_start: 0.7292 (m-10) cc_final: 0.7054 (m-10) REVERT: D 270 ASP cc_start: 0.8500 (m-30) cc_final: 0.8152 (m-30) REVERT: D 544 ILE cc_start: 0.7993 (mm) cc_final: 0.7675 (tt) outliers start: 45 outliers final: 35 residues processed: 195 average time/residue: 0.1253 time to fit residues: 41.6954 Evaluate side-chains 183 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 355 VAL Chi-restraints excluded: chain B residue 415 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 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 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 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 306 VAL 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 16 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.121440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074873 restraints weight = 44000.543| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.42 r_work: 0.2856 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22996 Z= 0.222 Angle : 0.631 9.386 31366 Z= 0.314 Chirality : 0.045 0.264 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.713 59.116 2920 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 18.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2700 helix: 0.63 (0.13), residues: 1620 sheet: -1.30 (0.76), residues: 42 loop : -1.98 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.016 0.002 TYR C 385 PHE 0.013 0.002 PHE C 683 TRP 0.008 0.001 TRP C 478 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (22946) covalent geometry : angle 0.62025 / 0.31 (31232) SS BOND : bond 0.00704 / 0.41 ( 10) SS BOND : angle 1.77371 / 1.06 ( 20) hydrogen bonds : bond 0.04829 / 3.13 ( 1048) hydrogen bonds : angle 4.17286 / 2.85 ( 3090) metal coordination : bond 0.00285 / 0.14 ( 2) link_BETA1-4 : bond 0.00389 / 0.25 ( 14) link_BETA1-4 : angle 1.57940 / 1.03 ( 42) link_NAG-ASN : bond 0.00399 / 0.27 ( 24) link_NAG-ASN : angle 2.07155 / 1.46 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 146 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 363 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7917 (mmtt) REVERT: A 401 HIS cc_start: 0.9604 (OUTLIER) cc_final: 0.8756 (t-90) REVERT: A 699 GLU cc_start: 0.8814 (mp0) cc_final: 0.8500 (mp0) REVERT: A 719 ASP cc_start: 0.8308 (t0) cc_final: 0.8082 (t0) REVERT: A 723 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: B 89 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8007 (mt-10) REVERT: B 209 TYR cc_start: 0.7208 (t80) cc_final: 0.6813 (t80) REVERT: B 224 TYR cc_start: 0.7290 (m-10) cc_final: 0.7069 (m-10) REVERT: B 270 ASP cc_start: 0.8540 (m-30) cc_final: 0.8186 (m-30) REVERT: B 436 MET cc_start: 0.8418 (mmm) cc_final: 0.8021 (tpt) REVERT: C 190 MET cc_start: 0.8923 (tmm) cc_final: 0.8614 (tmm) REVERT: C 363 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7965 (mmtt) REVERT: C 401 HIS cc_start: 0.9612 (OUTLIER) cc_final: 0.8756 (t-90) REVERT: C 719 ASP cc_start: 0.8306 (t0) cc_final: 0.8082 (t0) REVERT: C 723 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8784 (pt0) REVERT: D 85 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5924 (mm) REVERT: D 87 TYR cc_start: 0.6654 (t80) cc_final: 0.6338 (t80) REVERT: D 89 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7857 (mt-10) REVERT: D 209 TYR cc_start: 0.7196 (t80) cc_final: 0.6938 (t80) REVERT: D 224 TYR cc_start: 0.7224 (m-10) cc_final: 0.6995 (m-10) REVERT: D 270 ASP cc_start: 0.8546 (m-30) cc_final: 0.8190 (m-30) REVERT: D 544 ILE cc_start: 0.8022 (mm) cc_final: 0.7695 (tt) REVERT: B 701 MET cc_start: 0.6875 (mmt) cc_final: 0.6353 (mmt) outliers start: 66 outliers final: 41 residues processed: 205 average time/residue: 0.1177 time to fit residues: 40.6575 Evaluate side-chains 191 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 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 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 355 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 582 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 409 SER 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 55 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 306 VAL 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 545 ILE 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 43 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.122928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076457 restraints weight = 44386.748| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.46 r_work: 0.2885 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.146 Angle : 0.587 9.664 31366 Z= 0.292 Chirality : 0.042 0.255 3528 Planarity : 0.004 0.041 3912 Dihedral : 4.628 58.354 2920 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.18 % Allowed : 19.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2700 helix: 0.77 (0.13), residues: 1626 sheet: -1.24 (0.77), residues: 42 loop : -1.94 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.010 0.001 TYR C 516 PHE 0.010 0.001 PHE C 684 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22946) covalent geometry : angle 0.57712 / 0.29 (31232) SS BOND : bond 0.00666 / 0.39 ( 10) SS BOND : angle 1.63033 / 0.97 ( 20) hydrogen bonds : bond 0.04212 / 2.74 ( 1048) hydrogen bonds : angle 4.09277 / 2.80 ( 3090) metal coordination : bond 0.00207 / 0.10 ( 2) link_BETA1-4 : bond 0.00335 / 0.22 ( 14) link_BETA1-4 : angle 1.46098 / 0.95 ( 42) link_NAG-ASN : bond 0.00256 / 0.18 ( 24) link_NAG-ASN : angle 1.87365 / 1.34 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.698 Fit side-chains REVERT: A 115 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7614 (ttt90) REVERT: A 401 HIS cc_start: 0.9609 (OUTLIER) cc_final: 0.8817 (t-90) REVERT: A 699 GLU cc_start: 0.8820 (mp0) cc_final: 0.8508 (mp0) REVERT: A 719 ASP cc_start: 0.8225 (t0) cc_final: 0.7970 (t0) REVERT: A 723 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: B 89 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7978 (mt-10) REVERT: B 209 TYR cc_start: 0.7221 (t80) cc_final: 0.6879 (t80) REVERT: B 210 MET cc_start: 0.8309 (tmm) cc_final: 0.7976 (tmm) REVERT: B 224 TYR cc_start: 0.7263 (m-10) cc_final: 0.7053 (m-10) REVERT: B 270 ASP cc_start: 0.8532 (m-30) cc_final: 0.8180 (m-30) REVERT: B 436 MET cc_start: 0.8361 (mmm) cc_final: 0.7992 (tpt) REVERT: C 115 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7609 (ttt90) REVERT: C 190 MET cc_start: 0.8841 (tmm) cc_final: 0.8526 (tmm) REVERT: C 401 HIS cc_start: 0.9612 (OUTLIER) cc_final: 0.8818 (t-90) REVERT: C 719 ASP cc_start: 0.8222 (t0) cc_final: 0.7974 (t0) REVERT: C 723 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8750 (pt0) REVERT: D 85 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5948 (mm) REVERT: D 87 TYR cc_start: 0.6752 (t80) cc_final: 0.6474 (t80) REVERT: D 89 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7824 (mt-10) REVERT: D 209 TYR cc_start: 0.7164 (t80) cc_final: 0.6928 (t80) REVERT: D 224 TYR cc_start: 0.7247 (m-10) cc_final: 0.7025 (m-10) REVERT: D 270 ASP cc_start: 0.8533 (m-30) cc_final: 0.8183 (m-30) REVERT: D 544 ILE cc_start: 0.8105 (mm) cc_final: 0.7782 (tt) REVERT: B 701 MET cc_start: 0.6888 (mmt) cc_final: 0.6387 (mmt) REVERT: D 701 MET cc_start: 0.6994 (mmt) cc_final: 0.6664 (mmt) outliers start: 52 outliers final: 42 residues processed: 199 average time/residue: 0.1242 time to fit residues: 41.4795 Evaluate side-chains 196 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain A residue 409 SER 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 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 211 CYS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 415 LEU 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 554 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain C residue 115 ARG 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 409 SER 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 85 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 306 VAL 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 18 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.123452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077270 restraints weight = 44272.703| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.44 r_work: 0.2899 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.127 Angle : 0.577 11.209 31366 Z= 0.285 Chirality : 0.041 0.239 3528 Planarity : 0.004 0.041 3912 Dihedral : 4.525 58.897 2920 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.13 % Allowed : 19.41 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2700 helix: 0.91 (0.13), residues: 1632 sheet: -1.45 (0.75), residues: 42 loop : -1.91 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.011 0.001 TYR C 516 PHE 0.014 0.001 PHE B 546 TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22946) covalent geometry : angle 0.56773 / 0.28 (31232) SS BOND : bond 0.00682 / 0.39 ( 10) SS BOND : angle 1.60470 / 0.95 ( 20) hydrogen bonds : bond 0.03975 / 2.59 ( 1048) hydrogen bonds : angle 4.02353 / 2.76 ( 3090) metal coordination : bond 0.00079 / 0.04 ( 2) link_BETA1-4 : bond 0.00332 / 0.22 ( 14) link_BETA1-4 : angle 1.44004 / 0.94 ( 42) link_NAG-ASN : bond 0.00238 / 0.16 ( 24) link_NAG-ASN : angle 1.78053 / 1.28 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.869 Fit side-chains REVERT: A 401 HIS cc_start: 0.9563 (OUTLIER) cc_final: 0.8753 (t-90) REVERT: A 719 ASP cc_start: 0.8179 (t0) cc_final: 0.7943 (t0) REVERT: A 723 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: B 89 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7954 (mt-10) REVERT: B 209 TYR cc_start: 0.7271 (t80) cc_final: 0.6965 (t80) REVERT: B 210 MET cc_start: 0.8351 (tmm) cc_final: 0.8004 (tmm) REVERT: B 224 TYR cc_start: 0.7289 (m-10) cc_final: 0.7084 (m-10) REVERT: B 270 ASP cc_start: 0.8528 (m-30) cc_final: 0.8169 (m-30) REVERT: B 436 MET cc_start: 0.8364 (mmm) cc_final: 0.8024 (tpt) REVERT: C 190 MET cc_start: 0.8822 (tmm) cc_final: 0.8507 (tmm) REVERT: C 401 HIS cc_start: 0.9578 (OUTLIER) cc_final: 0.8786 (t-90) REVERT: C 520 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9090 (mp) REVERT: C 719 ASP cc_start: 0.8183 (t0) cc_final: 0.7956 (t0) REVERT: C 722 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8972 (tp) REVERT: C 723 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: D 85 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6177 (mm) REVERT: D 87 TYR cc_start: 0.6739 (t80) cc_final: 0.6492 (t80) REVERT: D 209 TYR cc_start: 0.7137 (t80) cc_final: 0.6893 (t80) REVERT: D 224 TYR cc_start: 0.7254 (m-10) cc_final: 0.7042 (m-10) REVERT: D 270 ASP cc_start: 0.8538 (m-30) cc_final: 0.8179 (m-30) REVERT: D 544 ILE cc_start: 0.8090 (mm) cc_final: 0.7760 (tt) REVERT: B 701 MET cc_start: 0.6841 (mmt) cc_final: 0.6382 (mmt) REVERT: D 701 MET cc_start: 0.6885 (mmt) cc_final: 0.6596 (mmt) outliers start: 51 outliers final: 38 residues processed: 204 average time/residue: 0.1238 time to fit residues: 42.8780 Evaluate side-chains 193 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL 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 626 SER Chi-restraints excluded: chain A residue 692 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 198 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 415 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 347 THR Chi-restraints excluded: chain C residue 365 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 506 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 520 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 722 LEU 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 85 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 306 VAL 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 43 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077221 restraints weight = 44187.091| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.46 r_work: 0.2900 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.003 0.041 22996 Z= 0.128 Angle : 0.580 11.012 31366 Z= 0.286 Chirality : 0.042 0.289 3528 Planarity : 0.004 0.040 3912 Dihedral : 4.498 58.925 2920 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.13 % Allowed : 19.54 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2700 helix: 0.99 (0.13), residues: 1626 sheet: -1.32 (0.77), residues: 42 loop : -1.85 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.011 0.001 TYR A 50 PHE 0.016 0.001 PHE B 90 TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22946) covalent geometry : angle 0.57155 / 0.28 (31232) SS BOND : bond 0.00639 / 0.37 ( 10) SS BOND : angle 1.48014 / 0.88 ( 20) hydrogen bonds : bond 0.03996 / 2.60 ( 1048) hydrogen bonds : angle 4.00423 / 2.75 ( 3090) metal coordination : bond 0.00133 / 0.07 ( 2) link_BETA1-4 : bond 0.00339 / 0.23 ( 14) link_BETA1-4 : angle 1.41538 / 0.93 ( 42) link_NAG-ASN : bond 0.00225 / 0.15 ( 24) link_NAG-ASN : angle 1.75341 / 1.26 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6846.06 seconds wall clock time: 117 minutes 19.10 seconds (7039.10 seconds total)