Starting phenix.real_space_refine on Thu Mar 5 01:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgs_34746/03_2026/8hgs_34746.map" } resolution = 3.81 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9900 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 6228 2.51 5 N 1768 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.14, per 1000 atoms: 0.21 Number of scatterers: 10080 At special positions: 0 Unit cell: (75.97, 129.47, 130.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 1958 8.00 N 1768 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 499 " distance=2.04 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 539 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 617 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-3 " NAG E 2 " - " BMA E 3 " " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG B 801 " - " ASN B 56 " " NAG B 802 " - " ASN B 175 " " NAG E 1 " - " ASN A 352 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 478.5 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 13.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.537A pdb=" N LYS A 80 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.638A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.823A pdb=" N CYS A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.805A pdb=" N CYS A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.521A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.712A pdb=" N LYS A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 4.203A pdb=" N PHE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.087A pdb=" N THR A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 removed outlier: 3.690A pdb=" N GLY A 434 " --> pdb=" O LYS A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.051A pdb=" N ALA A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.785A pdb=" N CYS A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.564A pdb=" N HIS C 10 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 11 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.565A pdb=" N HIS D 10 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 11 " --> pdb=" O LEU D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 11' Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.537A pdb=" N LYS B 80 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 81 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.639A pdb=" N GLY B 197 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 198 " --> pdb=" O PRO B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 198' Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.823A pdb=" N CYS B 207 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.804A pdb=" N CYS B 248 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.520A pdb=" N PHE B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 346' Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.712A pdb=" N LYS B 357 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.203A pdb=" N PHE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 4.087A pdb=" N THR B 397 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 removed outlier: 3.690A pdb=" N GLY B 434 " --> pdb=" O LYS B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 476 through 481 removed outlier: 4.039A pdb=" N LEU B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 4.051A pdb=" N ALA B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.785A pdb=" N CYS B 579 " --> pdb=" O PRO B 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS A 31 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 64 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 33 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU A 66 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 107 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS A 31 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 64 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 33 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU A 66 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N LEU A 90 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN A 94 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 69 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.640A pdb=" N GLN A 276 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.986A pdb=" N CYS A 337 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 369 through 371 removed outlier: 3.724A pdb=" N LEU A 406 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB4, first strand: chain 'A' and resid 548 through 551 Processing sheet with id=AB5, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AB6, first strand: chain 'A' and resid 597 through 599 removed outlier: 5.309A pdb=" N VAL A 607 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.539A pdb=" N CYS D 33 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AC1, first strand: chain 'B' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS B 31 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 64 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY B 33 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 66 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 107 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 33 removed outlier: 8.047A pdb=" N CYS B 31 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 64 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY B 33 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 66 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N LEU B 90 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 65 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA B 92 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 67 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN B 94 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR B 69 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 89 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 122 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 91 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 119 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER B 151 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 121 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 256 Processing sheet with id=AC4, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.640A pdb=" N GLN B 276 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AC6, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AC7, first strand: chain 'B' and resid 315 through 317 Processing sheet with id=AC8, first strand: chain 'B' and resid 337 through 338 removed outlier: 6.985A pdb=" N CYS B 337 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 369 through 371 removed outlier: 3.724A pdb=" N LEU B 406 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE B 462 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 439 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AD2, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AD3, first strand: chain 'B' and resid 548 through 551 Processing sheet with id=AD4, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AD5, first strand: chain 'B' and resid 597 through 599 removed outlier: 5.308A pdb=" N VAL B 607 " --> pdb=" O GLY B 598 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 252 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: 1.19 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3386 1.35 - 1.47: 2225 1.47 - 1.59: 4515 1.59 - 1.71: 2 1.71 - 1.83: 148 Bond restraints: 10276 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.591 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13492 1.90 - 3.81: 326 3.81 - 5.71: 56 5.71 - 7.61: 14 7.61 - 9.52: 8 Bond angle restraints: 13896 Sorted by residual: angle pdb=" N ALA A 258 " pdb=" CA ALA A 258 " pdb=" C ALA A 258 " ideal model delta sigma weight residual 114.64 108.32 6.32 1.52e+00 4.33e-01 1.73e+01 angle pdb=" N ALA B 258 " pdb=" CA ALA B 258 " pdb=" C ALA B 258 " ideal model delta sigma weight residual 114.64 108.33 6.31 1.52e+00 4.33e-01 1.72e+01 angle pdb=" C CYS B 470 " pdb=" N TYR B 471 " pdb=" CA TYR B 471 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C CYS A 470 " pdb=" N TYR A 471 " pdb=" CA TYR A 471 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N TYR A 471 " pdb=" CA TYR A 471 " pdb=" C TYR A 471 " ideal model delta sigma weight residual 110.80 118.50 -7.70 2.13e+00 2.20e-01 1.31e+01 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 6264 21.18 - 42.35: 170 42.35 - 63.53: 48 63.53 - 84.71: 26 84.71 - 105.88: 28 Dihedral angle restraints: 6536 sinusoidal: 2860 harmonic: 3676 Sorted by residual: dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 20 " pdb=" CB CYS D 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C 6 " pdb=" SG CYS C 6 " pdb=" SG CYS C 20 " pdb=" CB CYS C 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.02 -57.02 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -137.77 51.77 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 6533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1365 0.087 - 0.174: 175 0.174 - 0.261: 5 0.261 - 0.348: 3 0.348 - 0.436: 2 Chirality restraints: 1550 Sorted by residual: chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1547 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 256 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C ASP B 256 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 256 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ASP A 256 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 511 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO B 512 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.032 5.00e-02 4.00e+02 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3241 2.87 - 3.38: 8786 3.38 - 3.89: 16257 3.89 - 4.39: 17676 4.39 - 4.90: 30946 Nonbonded interactions: 76906 Sorted by model distance: nonbonded pdb=" OH TYR D 22 " pdb=" OD1 ASP D 27 " model vdw 2.368 3.040 nonbonded pdb=" OH TYR C 22 " pdb=" OD1 ASP C 27 " model vdw 2.368 3.040 nonbonded pdb=" OG1 THR A 302 " pdb=" OG SER A 306 " model vdw 2.379 3.040 nonbonded pdb=" O ARG B 309 " pdb=" NH1 ARG B 429 " model vdw 2.379 3.120 nonbonded pdb=" OG1 THR B 302 " pdb=" OG SER B 306 " model vdw 2.380 3.040 ... (remaining 76901 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 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 : 0.004 0.068 10340 Z= 0.205 Angle : 0.788 12.885 14036 Z= 0.405 Chirality : 0.057 0.436 1550 Planarity : 0.006 0.058 1814 Dihedral : 13.676 105.883 4020 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -3.50 (0.19), residues: 1272 helix: -3.75 (0.39), residues: 40 sheet: -3.30 (0.36), residues: 120 loop : -2.40 (0.15), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 222 TYR 0.013 0.001 TYR A 88 PHE 0.021 0.002 PHE A 404 TRP 0.005 0.001 TRP D 50 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00394 (10276) covalent geometry : angle 0.74831 (13896) SS BOND : bond 0.00330 ( 52) SS BOND : angle 1.08813 ( 104) hydrogen bonds : bond 0.21724 ( 138) hydrogen bonds : angle 6.98730 ( 252) link_ALPHA1-3 : bond 0.01502 ( 2) link_ALPHA1-3 : angle 2.28169 ( 6) link_BETA1-3 : bond 0.01574 ( 2) link_BETA1-3 : angle 7.29947 ( 6) link_BETA1-4 : bond 0.01613 ( 2) link_BETA1-4 : angle 1.91480 ( 6) link_NAG-ASN : bond 0.01039 ( 6) link_NAG-ASN : angle 4.99238 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7746 (mm110) cc_final: 0.7430 (mm-40) REVERT: A 46 ASP cc_start: 0.7171 (m-30) cc_final: 0.6741 (m-30) REVERT: A 59 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 64 ASN cc_start: 0.7707 (m-40) cc_final: 0.7225 (m-40) REVERT: A 88 TYR cc_start: 0.7328 (p90) cc_final: 0.7007 (p90) REVERT: A 93 LEU cc_start: 0.8190 (mt) cc_final: 0.7938 (mt) REVERT: A 105 GLN cc_start: 0.7984 (mt0) cc_final: 0.7562 (mt0) REVERT: A 126 ASP cc_start: 0.6266 (p0) cc_final: 0.5447 (p0) REVERT: A 130 THR cc_start: 0.6848 (p) cc_final: 0.6044 (p) REVERT: A 137 MET cc_start: 0.7581 (mtm) cc_final: 0.7354 (mtp) REVERT: A 139 ASN cc_start: 0.8003 (m-40) cc_final: 0.7336 (m-40) REVERT: A 149 ARG cc_start: 0.6534 (ttt90) cc_final: 0.6286 (ttt-90) REVERT: A 249 LEU cc_start: 0.7801 (mt) cc_final: 0.7517 (mt) REVERT: A 269 LEU cc_start: 0.6388 (mt) cc_final: 0.6102 (tp) REVERT: A 275 TYR cc_start: 0.8322 (m-80) cc_final: 0.8021 (m-80) REVERT: A 300 VAL cc_start: 0.8228 (t) cc_final: 0.8017 (t) REVERT: A 318 MET cc_start: 0.3937 (pp-130) cc_final: 0.3605 (pp-130) REVERT: A 399 LYS cc_start: 0.6567 (mtpp) cc_final: 0.6308 (mtpp) REVERT: A 422 ASN cc_start: 0.7591 (m-40) cc_final: 0.7137 (m-40) REVERT: A 452 SER cc_start: 0.6756 (p) cc_final: 0.6447 (t) REVERT: A 458 ASP cc_start: 0.7179 (t0) cc_final: 0.6800 (t0) REVERT: A 462 ILE cc_start: 0.6221 (tt) cc_final: 0.5918 (tt) REVERT: A 541 LEU cc_start: 0.6522 (mt) cc_final: 0.6225 (mp) REVERT: A 618 HIS cc_start: 0.6176 (m-70) cc_final: 0.5735 (m90) REVERT: C 21 MET cc_start: 0.7009 (ptt) cc_final: 0.6601 (ptt) REVERT: D 21 MET cc_start: 0.6977 (ptt) cc_final: 0.6640 (ptt) REVERT: D 40 GLU cc_start: 0.7091 (tt0) cc_final: 0.6812 (tt0) REVERT: B 37 LYS cc_start: 0.7442 (mttm) cc_final: 0.6922 (ttmt) REVERT: B 40 GLN cc_start: 0.7040 (tt0) cc_final: 0.6720 (tt0) REVERT: B 59 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 80 LYS cc_start: 0.8240 (mttt) cc_final: 0.7707 (mttt) REVERT: B 88 TYR cc_start: 0.7747 (p90) cc_final: 0.7511 (p90) REVERT: B 105 GLN cc_start: 0.7888 (mt0) cc_final: 0.7588 (mt0) REVERT: B 126 ASP cc_start: 0.6111 (p0) cc_final: 0.5486 (p0) REVERT: B 144 LEU cc_start: 0.8020 (mm) cc_final: 0.7809 (mp) REVERT: B 149 ARG cc_start: 0.6679 (ttt90) cc_final: 0.6327 (ttt90) REVERT: B 171 ASP cc_start: 0.7103 (t0) cc_final: 0.6698 (t0) REVERT: B 249 LEU cc_start: 0.7435 (mt) cc_final: 0.7232 (mt) REVERT: B 309 ARG cc_start: 0.6379 (mtt180) cc_final: 0.5865 (mtt-85) REVERT: B 318 MET cc_start: 0.4580 (pp-130) cc_final: 0.4113 (pp-130) REVERT: B 321 ASP cc_start: 0.5946 (m-30) cc_final: 0.5620 (m-30) REVERT: B 325 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7781 (mmtm) REVERT: B 345 PHE cc_start: 0.6638 (m-10) cc_final: 0.6354 (m-10) REVERT: B 360 LYS cc_start: 0.7949 (tppp) cc_final: 0.7713 (tppp) REVERT: B 369 LEU cc_start: 0.7280 (mt) cc_final: 0.7063 (mt) REVERT: B 399 LYS cc_start: 0.6562 (mtpp) cc_final: 0.6076 (mtpp) REVERT: B 400 GLU cc_start: 0.6942 (tt0) cc_final: 0.6672 (tt0) REVERT: B 427 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7726 (mmt90) REVERT: B 436 PHE cc_start: 0.5974 (m-80) cc_final: 0.5756 (m-80) REVERT: B 454 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7394 (mmtt) REVERT: B 458 ASP cc_start: 0.7467 (t0) cc_final: 0.6731 (t0) REVERT: B 460 ASP cc_start: 0.6374 (m-30) cc_final: 0.5770 (m-30) REVERT: B 471 TYR cc_start: 0.3317 (m-80) cc_final: 0.2441 (m-80) REVERT: B 475 ILE cc_start: 0.6263 (mm) cc_final: 0.6045 (mp) REVERT: B 521 ARG cc_start: 0.6689 (ppt-90) cc_final: 0.6430 (ppt-90) REVERT: B 551 GLU cc_start: 0.7579 (pt0) cc_final: 0.7152 (pt0) REVERT: B 557 GLN cc_start: 0.7171 (mt0) cc_final: 0.6690 (mt0) REVERT: B 600 MET cc_start: 0.6807 (tpp) cc_final: 0.6461 (tpp) REVERT: B 618 HIS cc_start: 0.6680 (m-70) cc_final: 0.6262 (m-70) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1241 time to fit residues: 53.0357 Evaluate side-chains 268 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 94 ASN A 139 ASN A 338 ASN A 432 GLN A 433 HIS A 468 ASN A 552 ASN A 559 HIS C 10 HIS D 10 HIS D 16 HIS B 47 HIS ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 432 GLN B 433 HIS B 468 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.175107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150721 restraints weight = 15546.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155339 restraints weight = 7912.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158405 restraints weight = 4843.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.160462 restraints weight = 3365.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.161940 restraints weight = 2568.510| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 10340 Z= 0.210 Angle : 0.788 13.954 14036 Z= 0.390 Chirality : 0.054 0.310 1550 Planarity : 0.005 0.066 1814 Dihedral : 13.195 84.404 1620 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.88 % Allowed : 8.66 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.59 (0.21), residues: 1272 helix: -0.60 (0.89), residues: 40 sheet: -2.54 (0.44), residues: 88 loop : -1.90 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.014 0.002 TYR A 88 PHE 0.022 0.002 PHE B 180 TRP 0.005 0.001 TRP B 410 HIS 0.006 0.002 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00476 (10276) covalent geometry : angle 0.74647 (13896) SS BOND : bond 0.00450 ( 52) SS BOND : angle 2.17137 ( 104) hydrogen bonds : bond 0.04159 ( 138) hydrogen bonds : angle 6.17498 ( 252) link_ALPHA1-3 : bond 0.01898 ( 2) link_ALPHA1-3 : angle 2.63909 ( 6) link_BETA1-3 : bond 0.00464 ( 2) link_BETA1-3 : angle 4.47990 ( 6) link_BETA1-4 : bond 0.00751 ( 2) link_BETA1-4 : angle 0.59962 ( 6) link_NAG-ASN : bond 0.00864 ( 6) link_NAG-ASN : angle 4.23216 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8157 (mttt) cc_final: 0.7905 (mttp) REVERT: A 46 ASP cc_start: 0.7301 (m-30) cc_final: 0.6799 (m-30) REVERT: A 54 MET cc_start: 0.7497 (tpp) cc_final: 0.7208 (tpp) REVERT: A 58 CYS cc_start: 0.5298 (t) cc_final: 0.5077 (t) REVERT: A 64 ASN cc_start: 0.8143 (m-40) cc_final: 0.7810 (m-40) REVERT: A 80 LYS cc_start: 0.7941 (mttt) cc_final: 0.7524 (mtmt) REVERT: A 105 GLN cc_start: 0.8045 (mt0) cc_final: 0.7671 (mt0) REVERT: A 108 ARG cc_start: 0.7571 (mtt-85) cc_final: 0.7096 (mmm-85) REVERT: A 139 ASN cc_start: 0.8020 (m110) cc_final: 0.7636 (m-40) REVERT: A 246 SER cc_start: 0.8262 (p) cc_final: 0.8044 (m) REVERT: A 253 LYS cc_start: 0.8036 (mttp) cc_final: 0.7136 (mttp) REVERT: A 255 ARG cc_start: 0.6974 (ttm-80) cc_final: 0.6732 (ttt-90) REVERT: A 340 ILE cc_start: 0.8107 (mp) cc_final: 0.7756 (mt) REVERT: A 350 SER cc_start: 0.6827 (t) cc_final: 0.6510 (p) REVERT: A 399 LYS cc_start: 0.6762 (mtpp) cc_final: 0.6473 (mtpp) REVERT: A 405 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7072 (tp) REVERT: A 422 ASN cc_start: 0.7828 (m-40) cc_final: 0.7444 (m-40) REVERT: A 436 PHE cc_start: 0.7483 (m-80) cc_final: 0.7217 (m-80) REVERT: A 548 GLU cc_start: 0.4902 (mp0) cc_final: 0.4327 (mp0) REVERT: A 559 HIS cc_start: 0.6673 (t-90) cc_final: 0.6424 (t-90) REVERT: A 574 ARG cc_start: 0.7241 (ptp90) cc_final: 0.6764 (mpp-170) REVERT: A 618 HIS cc_start: 0.6421 (m-70) cc_final: 0.6179 (m-70) REVERT: B 32 GLN cc_start: 0.7782 (mm110) cc_final: 0.7474 (mt0) REVERT: B 59 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 80 LYS cc_start: 0.8266 (mttt) cc_final: 0.7749 (mttt) REVERT: B 149 ARG cc_start: 0.7034 (ttt90) cc_final: 0.6807 (ttt90) REVERT: B 168 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7674 (p) REVERT: B 171 ASP cc_start: 0.6826 (t0) cc_final: 0.6522 (t0) REVERT: B 253 LYS cc_start: 0.8085 (mttp) cc_final: 0.7719 (mttp) REVERT: B 278 ASP cc_start: 0.7107 (m-30) cc_final: 0.6671 (m-30) REVERT: B 309 ARG cc_start: 0.6836 (mtt180) cc_final: 0.6373 (mmt90) REVERT: B 321 ASP cc_start: 0.5995 (m-30) cc_final: 0.5218 (m-30) REVERT: B 345 PHE cc_start: 0.7512 (m-10) cc_final: 0.7081 (m-10) REVERT: B 364 SER cc_start: 0.8693 (p) cc_final: 0.8464 (m) REVERT: B 369 LEU cc_start: 0.8241 (mt) cc_final: 0.7861 (mt) REVERT: B 399 LYS cc_start: 0.6925 (mtpp) cc_final: 0.6413 (mtpp) REVERT: B 400 GLU cc_start: 0.7148 (tt0) cc_final: 0.6882 (tt0) REVERT: B 452 SER cc_start: 0.6730 (p) cc_final: 0.5739 (p) REVERT: B 454 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7596 (mmtt) REVERT: B 458 ASP cc_start: 0.7665 (t0) cc_final: 0.7055 (t0) REVERT: B 460 ASP cc_start: 0.6306 (m-30) cc_final: 0.5797 (m-30) REVERT: B 475 ILE cc_start: 0.6731 (mm) cc_final: 0.6513 (mp) REVERT: B 487 LYS cc_start: 0.7149 (pttp) cc_final: 0.6535 (pttp) REVERT: B 521 ARG cc_start: 0.6852 (ppt-90) cc_final: 0.6555 (ppt-90) REVERT: B 618 HIS cc_start: 0.6500 (m-70) cc_final: 0.6295 (m90) outliers start: 21 outliers final: 10 residues processed: 307 average time/residue: 0.1245 time to fit residues: 49.3901 Evaluate side-chains 294 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 282 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 206 ASN A 408 GLN A 444 ASN A 493 ASN C 10 HIS C 16 HIS D 10 HIS B 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 444 ASN B 559 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136694 restraints weight = 15054.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141124 restraints weight = 7636.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.144100 restraints weight = 4681.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146132 restraints weight = 3258.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147352 restraints weight = 2493.210| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10340 Z= 0.286 Angle : 0.861 9.544 14036 Z= 0.434 Chirality : 0.055 0.331 1550 Planarity : 0.005 0.074 1814 Dihedral : 10.295 70.100 1620 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.50 % Allowed : 10.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.21 (0.22), residues: 1272 helix: -0.55 (0.93), residues: 42 sheet: -2.54 (0.53), residues: 64 loop : -1.61 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 533 TYR 0.023 0.002 TYR A 125 PHE 0.017 0.003 PHE A 78 TRP 0.020 0.002 TRP C 49 HIS 0.009 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00598 (10276) covalent geometry : angle 0.83148 (13896) SS BOND : bond 0.00851 ( 52) SS BOND : angle 1.74302 ( 104) hydrogen bonds : bond 0.04522 ( 138) hydrogen bonds : angle 6.54922 ( 252) link_ALPHA1-3 : bond 0.01849 ( 2) link_ALPHA1-3 : angle 2.66941 ( 6) link_BETA1-3 : bond 0.00402 ( 2) link_BETA1-3 : angle 3.22663 ( 6) link_BETA1-4 : bond 0.00617 ( 2) link_BETA1-4 : angle 1.68716 ( 6) link_NAG-ASN : bond 0.01115 ( 6) link_NAG-ASN : angle 4.46194 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8197 (mm110) cc_final: 0.7940 (mp10) REVERT: A 34 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7432 (p) REVERT: A 37 LYS cc_start: 0.8212 (mttt) cc_final: 0.7831 (mttm) REVERT: A 46 ASP cc_start: 0.7337 (m-30) cc_final: 0.6880 (m-30) REVERT: A 58 CYS cc_start: 0.5339 (t) cc_final: 0.5096 (t) REVERT: A 59 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 64 ASN cc_start: 0.8269 (m-40) cc_final: 0.7717 (m-40) REVERT: A 66 GLU cc_start: 0.5879 (mt-10) cc_final: 0.5581 (mt-10) REVERT: A 80 LYS cc_start: 0.8313 (mttt) cc_final: 0.7670 (mmtt) REVERT: A 105 GLN cc_start: 0.8244 (mt0) cc_final: 0.7946 (mt0) REVERT: A 111 MET cc_start: 0.7227 (ptm) cc_final: 0.7022 (ptm) REVERT: A 139 ASN cc_start: 0.8190 (m110) cc_final: 0.7960 (m-40) REVERT: A 149 ARG cc_start: 0.6849 (ttt-90) cc_final: 0.6643 (ttt-90) REVERT: A 210 LEU cc_start: 0.8405 (mm) cc_final: 0.8105 (mm) REVERT: A 222 ARG cc_start: 0.6181 (mtp85) cc_final: 0.5743 (mtt90) REVERT: A 235 GLN cc_start: 0.7662 (mm-40) cc_final: 0.6679 (mm-40) REVERT: A 252 ARG cc_start: 0.7101 (ttt-90) cc_final: 0.6539 (ttp80) REVERT: A 256 ASP cc_start: 0.6446 (m-30) cc_final: 0.6079 (m-30) REVERT: A 263 THR cc_start: 0.8460 (p) cc_final: 0.8252 (p) REVERT: A 299 TYR cc_start: 0.7986 (m-80) cc_final: 0.7465 (m-80) REVERT: A 335 LYS cc_start: 0.7600 (tptp) cc_final: 0.7283 (tptp) REVERT: A 340 ILE cc_start: 0.8435 (mp) cc_final: 0.8048 (mt) REVERT: A 350 SER cc_start: 0.6918 (t) cc_final: 0.6701 (p) REVERT: A 357 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7746 (mtmm) REVERT: A 399 LYS cc_start: 0.7285 (mtpp) cc_final: 0.6909 (mtpp) REVERT: A 405 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6871 (tp) REVERT: A 426 ILE cc_start: 0.8036 (mt) cc_final: 0.7429 (tt) REVERT: A 458 ASP cc_start: 0.7734 (t0) cc_final: 0.7242 (t0) REVERT: A 460 ASP cc_start: 0.6414 (m-30) cc_final: 0.6158 (m-30) REVERT: A 521 ARG cc_start: 0.7372 (ppt-90) cc_final: 0.7080 (ptt-90) REVERT: A 561 GLU cc_start: 0.6279 (tp30) cc_final: 0.3350 (mm-30) REVERT: A 618 HIS cc_start: 0.6954 (m-70) cc_final: 0.6471 (m170) REVERT: B 32 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7623 (mt0) REVERT: B 54 MET cc_start: 0.8186 (tpp) cc_final: 0.7569 (tpp) REVERT: B 59 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 66 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 80 LYS cc_start: 0.8381 (mttt) cc_final: 0.7765 (mttt) REVERT: B 112 TYR cc_start: 0.7651 (m-80) cc_final: 0.6613 (m-80) REVERT: B 139 ASN cc_start: 0.7846 (m110) cc_final: 0.7596 (m-40) REVERT: B 168 VAL cc_start: 0.8400 (t) cc_final: 0.8063 (p) REVERT: B 171 ASP cc_start: 0.7058 (t0) cc_final: 0.6632 (t0) REVERT: B 210 LEU cc_start: 0.8324 (mt) cc_final: 0.8093 (mm) REVERT: B 235 GLN cc_start: 0.7615 (mp10) cc_final: 0.7089 (mm110) REVERT: B 260 CYS cc_start: 0.5922 (OUTLIER) cc_final: 0.4770 (m) REVERT: B 271 ASN cc_start: 0.7916 (t0) cc_final: 0.7495 (m-40) REVERT: B 285 TYR cc_start: 0.7600 (m-80) cc_final: 0.7334 (m-80) REVERT: B 286 SER cc_start: 0.7164 (m) cc_final: 0.6795 (m) REVERT: B 309 ARG cc_start: 0.7499 (mtt180) cc_final: 0.6809 (mtt-85) REVERT: B 364 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8505 (m) REVERT: B 382 THR cc_start: 0.2146 (OUTLIER) cc_final: 0.1901 (m) REVERT: B 396 LYS cc_start: 0.7804 (mttt) cc_final: 0.7102 (mttm) REVERT: B 399 LYS cc_start: 0.7105 (mtpp) cc_final: 0.6644 (mtpp) REVERT: B 415 THR cc_start: 0.7666 (p) cc_final: 0.7364 (t) REVERT: B 427 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7873 (mmt90) REVERT: B 451 ARG cc_start: 0.7589 (ptp90) cc_final: 0.6201 (ptp90) REVERT: B 454 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7665 (mmtt) REVERT: B 460 ASP cc_start: 0.6436 (m-30) cc_final: 0.6170 (m-30) REVERT: B 487 LYS cc_start: 0.7587 (pttp) cc_final: 0.6962 (pttp) REVERT: B 502 THR cc_start: 0.8105 (p) cc_final: 0.7832 (t) REVERT: B 559 HIS cc_start: 0.7195 (t-90) cc_final: 0.6683 (t-90) REVERT: B 618 HIS cc_start: 0.7120 (m-70) cc_final: 0.6810 (m-70) outliers start: 28 outliers final: 11 residues processed: 330 average time/residue: 0.1200 time to fit residues: 52.2135 Evaluate side-chains 314 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 361 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 466 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135104 restraints weight = 15227.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139478 restraints weight = 7571.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142363 restraints weight = 4572.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144314 restraints weight = 3162.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145694 restraints weight = 2410.481| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10340 Z= 0.227 Angle : 0.832 16.029 14036 Z= 0.404 Chirality : 0.053 0.330 1550 Planarity : 0.005 0.052 1814 Dihedral : 9.227 65.121 1620 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.68 % Allowed : 13.84 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.10 (0.22), residues: 1272 helix: -0.82 (0.89), residues: 40 sheet: -2.22 (0.56), residues: 74 loop : -1.52 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.014 0.002 TYR D 37 PHE 0.024 0.002 PHE B 48 TRP 0.031 0.002 TRP C 49 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00501 (10276) covalent geometry : angle 0.79189 (13896) SS BOND : bond 0.00458 ( 52) SS BOND : angle 2.15088 ( 104) hydrogen bonds : bond 0.03964 ( 138) hydrogen bonds : angle 6.53230 ( 252) link_ALPHA1-3 : bond 0.02175 ( 2) link_ALPHA1-3 : angle 2.73766 ( 6) link_BETA1-3 : bond 0.00461 ( 2) link_BETA1-3 : angle 3.11158 ( 6) link_BETA1-4 : bond 0.00530 ( 2) link_BETA1-4 : angle 1.58675 ( 6) link_NAG-ASN : bond 0.00806 ( 6) link_NAG-ASN : angle 4.67909 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8151 (mm110) cc_final: 0.7862 (mm-40) REVERT: A 37 LYS cc_start: 0.8271 (mttt) cc_final: 0.7845 (mttm) REVERT: A 46 ASP cc_start: 0.7296 (m-30) cc_final: 0.6889 (m-30) REVERT: A 54 MET cc_start: 0.7805 (tpp) cc_final: 0.7398 (tpp) REVERT: A 58 CYS cc_start: 0.5233 (t) cc_final: 0.5006 (t) REVERT: A 59 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 64 ASN cc_start: 0.8293 (m-40) cc_final: 0.7740 (m-40) REVERT: A 80 LYS cc_start: 0.8331 (mttt) cc_final: 0.7858 (mtmt) REVERT: A 105 GLN cc_start: 0.8254 (mt0) cc_final: 0.7939 (mt0) REVERT: A 210 LEU cc_start: 0.8414 (mm) cc_final: 0.8108 (mm) REVERT: A 222 ARG cc_start: 0.6330 (mtp85) cc_final: 0.5927 (mtt90) REVERT: A 252 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6344 (ttp-110) REVERT: A 260 CYS cc_start: 0.6017 (OUTLIER) cc_final: 0.4488 (m) REVERT: A 297 ARG cc_start: 0.7010 (mmm-85) cc_final: 0.6771 (mtp85) REVERT: A 299 TYR cc_start: 0.7946 (m-80) cc_final: 0.7370 (m-80) REVERT: A 335 LYS cc_start: 0.7638 (tptp) cc_final: 0.7356 (tptp) REVERT: A 340 ILE cc_start: 0.8315 (mp) cc_final: 0.7955 (mt) REVERT: A 357 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7829 (mtmm) REVERT: A 382 THR cc_start: 0.1399 (OUTLIER) cc_final: 0.1178 (m) REVERT: A 399 LYS cc_start: 0.7173 (mtpp) cc_final: 0.6841 (mtpp) REVERT: A 405 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6841 (tp) REVERT: A 426 ILE cc_start: 0.8047 (mt) cc_final: 0.7391 (tt) REVERT: A 454 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7545 (mmtt) REVERT: A 458 ASP cc_start: 0.7763 (t0) cc_final: 0.7307 (t0) REVERT: A 489 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7659 (mtmt) REVERT: A 548 GLU cc_start: 0.4416 (mp0) cc_final: 0.3744 (mp0) REVERT: A 618 HIS cc_start: 0.7129 (m-70) cc_final: 0.6651 (m-70) REVERT: C 44 TYR cc_start: 0.7404 (m-10) cc_final: 0.7124 (m-10) REVERT: B 32 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7600 (mt0) REVERT: B 59 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 66 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6541 (mt-10) REVERT: B 80 LYS cc_start: 0.8396 (mttt) cc_final: 0.7797 (mttt) REVERT: B 98 ARG cc_start: 0.7552 (ttt90) cc_final: 0.7238 (mtp-110) REVERT: B 111 MET cc_start: 0.7009 (ptm) cc_final: 0.6802 (ptm) REVERT: B 168 VAL cc_start: 0.8245 (t) cc_final: 0.7916 (p) REVERT: B 171 ASP cc_start: 0.7050 (t0) cc_final: 0.6499 (t0) REVERT: B 172 PHE cc_start: 0.8033 (m-10) cc_final: 0.7371 (m-10) REVERT: B 235 GLN cc_start: 0.7639 (mp10) cc_final: 0.6785 (mm110) REVERT: B 252 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6616 (ttt-90) REVERT: B 261 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7102 (mmtt) REVERT: B 263 THR cc_start: 0.8545 (m) cc_final: 0.8236 (p) REVERT: B 271 ASN cc_start: 0.7902 (t0) cc_final: 0.7437 (m-40) REVERT: B 286 SER cc_start: 0.7200 (m) cc_final: 0.6870 (m) REVERT: B 345 PHE cc_start: 0.8058 (m-10) cc_final: 0.7715 (m-10) REVERT: B 364 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 369 LEU cc_start: 0.8350 (mt) cc_final: 0.8074 (mt) REVERT: B 382 THR cc_start: 0.2548 (OUTLIER) cc_final: 0.2277 (m) REVERT: B 396 LYS cc_start: 0.7743 (mttt) cc_final: 0.7128 (mttm) REVERT: B 399 LYS cc_start: 0.7097 (mtpp) cc_final: 0.6648 (mtpp) REVERT: B 404 PHE cc_start: 0.8156 (p90) cc_final: 0.7403 (p90) REVERT: B 454 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7666 (mmtt) REVERT: B 458 ASP cc_start: 0.7829 (t0) cc_final: 0.7162 (t0) REVERT: B 487 LYS cc_start: 0.7714 (pttp) cc_final: 0.7312 (pttp) REVERT: B 502 THR cc_start: 0.8143 (p) cc_final: 0.7857 (t) REVERT: B 553 SER cc_start: 0.8023 (m) cc_final: 0.7822 (t) REVERT: B 559 HIS cc_start: 0.7359 (t-90) cc_final: 0.7011 (t-90) REVERT: B 581 GLN cc_start: 0.7699 (tt0) cc_final: 0.7354 (tm-30) REVERT: B 618 HIS cc_start: 0.7115 (m-70) cc_final: 0.6730 (m90) outliers start: 30 outliers final: 17 residues processed: 296 average time/residue: 0.1248 time to fit residues: 48.1927 Evaluate side-chains 295 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 chunk 111 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 361 ASN A 504 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134308 restraints weight = 15262.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138727 restraints weight = 7679.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141660 restraints weight = 4684.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143679 restraints weight = 3250.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144939 restraints weight = 2472.049| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10340 Z= 0.166 Angle : 0.759 10.742 14036 Z= 0.372 Chirality : 0.050 0.333 1550 Planarity : 0.004 0.049 1814 Dihedral : 8.413 57.822 1620 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.50 % Allowed : 14.55 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.23), residues: 1272 helix: -0.97 (0.87), residues: 40 sheet: -1.97 (0.66), residues: 54 loop : -1.37 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 533 TYR 0.020 0.002 TYR C 37 PHE 0.023 0.002 PHE A 172 TRP 0.043 0.002 TRP C 49 HIS 0.006 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00368 (10276) covalent geometry : angle 0.72252 (13896) SS BOND : bond 0.00419 ( 52) SS BOND : angle 1.80338 ( 104) hydrogen bonds : bond 0.03733 ( 138) hydrogen bonds : angle 6.30392 ( 252) link_ALPHA1-3 : bond 0.02308 ( 2) link_ALPHA1-3 : angle 3.04776 ( 6) link_BETA1-3 : bond 0.00665 ( 2) link_BETA1-3 : angle 2.90939 ( 6) link_BETA1-4 : bond 0.00658 ( 2) link_BETA1-4 : angle 1.80062 ( 6) link_NAG-ASN : bond 0.00581 ( 6) link_NAG-ASN : angle 4.46597 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8082 (mm110) cc_final: 0.7541 (mt0) REVERT: A 58 CYS cc_start: 0.5272 (t) cc_final: 0.5021 (t) REVERT: A 59 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 64 ASN cc_start: 0.8272 (m-40) cc_final: 0.7669 (m-40) REVERT: A 80 LYS cc_start: 0.8359 (mttt) cc_final: 0.7678 (mttt) REVERT: A 83 GLN cc_start: 0.7320 (mt0) cc_final: 0.6815 (mt0) REVERT: A 105 GLN cc_start: 0.8258 (mt0) cc_final: 0.8021 (mt0) REVERT: A 125 TYR cc_start: 0.7877 (p90) cc_final: 0.7485 (p90) REVERT: A 171 ASP cc_start: 0.6543 (t0) cc_final: 0.6067 (t0) REVERT: A 172 PHE cc_start: 0.7891 (m-10) cc_final: 0.7163 (m-10) REVERT: A 210 LEU cc_start: 0.8405 (mm) cc_final: 0.8151 (mm) REVERT: A 222 ARG cc_start: 0.6401 (mtp85) cc_final: 0.6024 (mtt90) REVERT: A 252 ARG cc_start: 0.7226 (ttt-90) cc_final: 0.6754 (ttp80) REVERT: A 253 LYS cc_start: 0.8182 (mttp) cc_final: 0.7171 (mttp) REVERT: A 260 CYS cc_start: 0.6169 (OUTLIER) cc_final: 0.4703 (m) REVERT: A 335 LYS cc_start: 0.7544 (tptp) cc_final: 0.7273 (tptp) REVERT: A 340 ILE cc_start: 0.8314 (mp) cc_final: 0.7960 (mt) REVERT: A 357 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7763 (mtmm) REVERT: A 382 THR cc_start: 0.1658 (OUTLIER) cc_final: 0.1453 (m) REVERT: A 399 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6777 (mtpp) REVERT: A 405 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 454 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7509 (mmtt) REVERT: A 458 ASP cc_start: 0.7869 (t0) cc_final: 0.7383 (t0) REVERT: A 521 ARG cc_start: 0.7439 (ppt-90) cc_final: 0.7216 (ptt-90) REVERT: A 548 GLU cc_start: 0.3330 (mp0) cc_final: 0.2922 (mp0) REVERT: A 586 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6765 (tp) REVERT: A 618 HIS cc_start: 0.6986 (m-70) cc_final: 0.6482 (m-70) REVERT: D 47 LEU cc_start: 0.6760 (mt) cc_final: 0.6471 (mt) REVERT: B 32 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7585 (mt0) REVERT: B 59 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 66 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6525 (mt-10) REVERT: B 80 LYS cc_start: 0.8398 (mttt) cc_final: 0.7775 (mttt) REVERT: B 98 ARG cc_start: 0.7621 (ttt90) cc_final: 0.7179 (mmm-85) REVERT: B 168 VAL cc_start: 0.8247 (t) cc_final: 0.7932 (p) REVERT: B 171 ASP cc_start: 0.7061 (t0) cc_final: 0.6508 (t0) REVERT: B 172 PHE cc_start: 0.7993 (m-10) cc_final: 0.7433 (m-10) REVERT: B 210 LEU cc_start: 0.8409 (mm) cc_final: 0.7814 (tp) REVERT: B 252 ARG cc_start: 0.7115 (ttt-90) cc_final: 0.6914 (ttp80) REVERT: B 253 LYS cc_start: 0.8167 (tttm) cc_final: 0.7833 (tttm) REVERT: B 263 THR cc_start: 0.8487 (m) cc_final: 0.8190 (p) REVERT: B 271 ASN cc_start: 0.7937 (t0) cc_final: 0.7311 (m-40) REVERT: B 286 SER cc_start: 0.7158 (m) cc_final: 0.6822 (m) REVERT: B 350 SER cc_start: 0.6829 (t) cc_final: 0.6604 (p) REVERT: B 364 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8530 (m) REVERT: B 369 LEU cc_start: 0.8271 (mt) cc_final: 0.7942 (mt) REVERT: B 382 THR cc_start: 0.2698 (OUTLIER) cc_final: 0.2453 (m) REVERT: B 396 LYS cc_start: 0.7718 (mttt) cc_final: 0.7061 (mttm) REVERT: B 399 LYS cc_start: 0.6992 (mtpp) cc_final: 0.6583 (mtpp) REVERT: B 454 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7653 (mmtt) REVERT: B 458 ASP cc_start: 0.7819 (t0) cc_final: 0.7331 (t0) REVERT: B 487 LYS cc_start: 0.7720 (pttp) cc_final: 0.7318 (pttp) REVERT: B 502 THR cc_start: 0.8198 (p) cc_final: 0.7943 (t) REVERT: B 534 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6652 (mp0) REVERT: B 618 HIS cc_start: 0.7103 (m-70) cc_final: 0.6665 (m90) outliers start: 28 outliers final: 17 residues processed: 298 average time/residue: 0.1174 time to fit residues: 46.3607 Evaluate side-chains 301 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 112 optimal weight: 0.0170 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133158 restraints weight = 15304.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137545 restraints weight = 7668.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140463 restraints weight = 4666.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142395 restraints weight = 3239.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143829 restraints weight = 2476.143| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10340 Z= 0.190 Angle : 0.771 10.907 14036 Z= 0.375 Chirality : 0.051 0.332 1550 Planarity : 0.004 0.042 1814 Dihedral : 8.007 55.924 1620 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.68 % Allowed : 16.52 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.23), residues: 1272 helix: -1.16 (0.84), residues: 40 sheet: -1.96 (0.70), residues: 54 loop : -1.25 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 149 TYR 0.023 0.002 TYR C 37 PHE 0.025 0.002 PHE A 404 TRP 0.045 0.002 TRP C 49 HIS 0.004 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00414 (10276) covalent geometry : angle 0.73599 (13896) SS BOND : bond 0.00461 ( 52) SS BOND : angle 1.61085 ( 104) hydrogen bonds : bond 0.03771 ( 138) hydrogen bonds : angle 6.33586 ( 252) link_ALPHA1-3 : bond 0.02515 ( 2) link_ALPHA1-3 : angle 3.29345 ( 6) link_BETA1-3 : bond 0.00482 ( 2) link_BETA1-3 : angle 2.84852 ( 6) link_BETA1-4 : bond 0.00667 ( 2) link_BETA1-4 : angle 1.94205 ( 6) link_NAG-ASN : bond 0.00731 ( 6) link_NAG-ASN : angle 4.72767 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8020 (mm110) cc_final: 0.7582 (mt0) REVERT: A 58 CYS cc_start: 0.5226 (t) cc_final: 0.4949 (t) REVERT: A 59 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 80 LYS cc_start: 0.8381 (mttt) cc_final: 0.7715 (mtmt) REVERT: A 83 GLN cc_start: 0.7349 (mt0) cc_final: 0.6830 (mt0) REVERT: A 124 ASN cc_start: 0.8068 (m-40) cc_final: 0.7630 (m-40) REVERT: A 125 TYR cc_start: 0.7933 (p90) cc_final: 0.7578 (p90) REVERT: A 149 ARG cc_start: 0.6849 (mmm-85) cc_final: 0.6626 (mtp-110) REVERT: A 165 ARG cc_start: 0.7679 (ttt180) cc_final: 0.7375 (ttt180) REVERT: A 171 ASP cc_start: 0.6657 (t0) cc_final: 0.6154 (t0) REVERT: A 172 PHE cc_start: 0.7928 (m-10) cc_final: 0.7281 (m-10) REVERT: A 210 LEU cc_start: 0.8476 (mm) cc_final: 0.8250 (mm) REVERT: A 252 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6581 (ttp80) REVERT: A 253 LYS cc_start: 0.8081 (mttp) cc_final: 0.7621 (mttp) REVERT: A 260 CYS cc_start: 0.6647 (OUTLIER) cc_final: 0.4863 (m) REVERT: A 335 LYS cc_start: 0.7524 (tptp) cc_final: 0.7292 (tptp) REVERT: A 340 ILE cc_start: 0.8334 (mp) cc_final: 0.7990 (mt) REVERT: A 357 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7775 (mtmm) REVERT: A 361 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6576 (t0) REVERT: A 382 THR cc_start: 0.2212 (OUTLIER) cc_final: 0.1982 (m) REVERT: A 399 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6865 (mtpp) REVERT: A 405 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7111 (tp) REVERT: A 454 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7536 (mmtt) REVERT: A 458 ASP cc_start: 0.7898 (t0) cc_final: 0.7388 (t0) REVERT: A 489 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7605 (mtmt) REVERT: A 521 ARG cc_start: 0.7502 (ppt-90) cc_final: 0.6943 (ppt-90) REVERT: A 548 GLU cc_start: 0.3386 (mp0) cc_final: 0.2663 (mp0) REVERT: A 561 GLU cc_start: 0.5754 (tp30) cc_final: 0.4643 (mm-30) REVERT: A 618 HIS cc_start: 0.7099 (m-70) cc_final: 0.6527 (m170) REVERT: D 37 TYR cc_start: 0.8465 (m-10) cc_final: 0.8186 (m-10) REVERT: B 32 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7532 (mt0) REVERT: B 59 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 66 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6181 (mt-10) REVERT: B 80 LYS cc_start: 0.8440 (mttt) cc_final: 0.7803 (mttt) REVERT: B 139 ASN cc_start: 0.7818 (m110) cc_final: 0.7607 (m-40) REVERT: B 168 VAL cc_start: 0.8310 (t) cc_final: 0.7959 (p) REVERT: B 171 ASP cc_start: 0.7164 (t0) cc_final: 0.6609 (t0) REVERT: B 172 PHE cc_start: 0.7991 (m-10) cc_final: 0.7462 (m-10) REVERT: B 210 LEU cc_start: 0.8418 (mm) cc_final: 0.7824 (tp) REVERT: B 252 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6861 (ttp-110) REVERT: B 253 LYS cc_start: 0.8177 (tttm) cc_final: 0.7800 (tttp) REVERT: B 261 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7182 (mmtt) REVERT: B 263 THR cc_start: 0.8493 (m) cc_final: 0.8200 (p) REVERT: B 271 ASN cc_start: 0.7927 (t0) cc_final: 0.7269 (m-40) REVERT: B 286 SER cc_start: 0.7108 (m) cc_final: 0.6803 (m) REVERT: B 364 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8519 (m) REVERT: B 382 THR cc_start: 0.3201 (OUTLIER) cc_final: 0.2937 (m) REVERT: B 396 LYS cc_start: 0.7711 (mttt) cc_final: 0.7279 (mttm) REVERT: B 399 LYS cc_start: 0.7087 (mtpp) cc_final: 0.6616 (mtpp) REVERT: B 415 THR cc_start: 0.7652 (p) cc_final: 0.7135 (t) REVERT: B 427 ARG cc_start: 0.8206 (mmt90) cc_final: 0.7725 (mmt90) REVERT: B 454 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7667 (mmtt) REVERT: B 458 ASP cc_start: 0.7856 (t0) cc_final: 0.7362 (t0) REVERT: B 487 LYS cc_start: 0.7819 (pttp) cc_final: 0.7404 (pttp) REVERT: B 502 THR cc_start: 0.8243 (p) cc_final: 0.7969 (t) REVERT: B 561 GLU cc_start: 0.6648 (tp30) cc_final: 0.6445 (tp30) REVERT: B 618 HIS cc_start: 0.6911 (m-70) cc_final: 0.6545 (m90) outliers start: 30 outliers final: 17 residues processed: 312 average time/residue: 0.1361 time to fit residues: 54.6136 Evaluate side-chains 311 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9980 chunk 117 optimal weight: 0.0030 chunk 103 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132485 restraints weight = 15062.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136888 restraints weight = 7661.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139840 restraints weight = 4695.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141871 restraints weight = 3270.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143220 restraints weight = 2494.034| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10340 Z= 0.179 Angle : 0.764 9.863 14036 Z= 0.371 Chirality : 0.051 0.336 1550 Planarity : 0.004 0.037 1814 Dihedral : 7.747 55.923 1620 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.86 % Allowed : 17.50 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1272 helix: -1.07 (0.85), residues: 38 sheet: -2.01 (0.68), residues: 54 loop : -1.21 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.019 0.002 TYR C 37 PHE 0.028 0.002 PHE A 404 TRP 0.046 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00390 (10276) covalent geometry : angle 0.73161 (13896) SS BOND : bond 0.00446 ( 52) SS BOND : angle 1.42441 ( 104) hydrogen bonds : bond 0.03729 ( 138) hydrogen bonds : angle 6.25362 ( 252) link_ALPHA1-3 : bond 0.02548 ( 2) link_ALPHA1-3 : angle 3.49112 ( 6) link_BETA1-3 : bond 0.00281 ( 2) link_BETA1-3 : angle 2.91991 ( 6) link_BETA1-4 : bond 0.00846 ( 2) link_BETA1-4 : angle 2.03819 ( 6) link_NAG-ASN : bond 0.00673 ( 6) link_NAG-ASN : angle 4.72775 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7992 (mm110) cc_final: 0.7571 (mt0) REVERT: A 58 CYS cc_start: 0.5252 (t) cc_final: 0.4938 (t) REVERT: A 59 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 80 LYS cc_start: 0.8374 (mttt) cc_final: 0.7684 (mttt) REVERT: A 83 GLN cc_start: 0.7310 (mt0) cc_final: 0.6728 (mt0) REVERT: A 125 TYR cc_start: 0.7918 (p90) cc_final: 0.7681 (p90) REVERT: A 149 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6708 (mtp-110) REVERT: A 165 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7345 (ttt180) REVERT: A 171 ASP cc_start: 0.6671 (t0) cc_final: 0.6150 (t0) REVERT: A 172 PHE cc_start: 0.7883 (m-10) cc_final: 0.7278 (m-10) REVERT: A 210 LEU cc_start: 0.8467 (mm) cc_final: 0.8233 (mm) REVERT: A 252 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6659 (ttp-110) REVERT: A 335 LYS cc_start: 0.7581 (tptp) cc_final: 0.7353 (tptp) REVERT: A 340 ILE cc_start: 0.8313 (mp) cc_final: 0.7984 (mt) REVERT: A 357 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7772 (mtmm) REVERT: A 382 THR cc_start: 0.2283 (OUTLIER) cc_final: 0.2045 (m) REVERT: A 399 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6870 (mtpp) REVERT: A 405 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7124 (tp) REVERT: A 454 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7551 (mmtt) REVERT: A 458 ASP cc_start: 0.7825 (t0) cc_final: 0.7355 (t0) REVERT: A 489 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7604 (mtmt) REVERT: A 521 ARG cc_start: 0.7509 (ppt-90) cc_final: 0.7021 (ppt-90) REVERT: A 548 GLU cc_start: 0.3411 (mp0) cc_final: 0.2838 (mp0) REVERT: A 561 GLU cc_start: 0.5820 (tp30) cc_final: 0.4705 (mm-30) REVERT: A 586 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6713 (tp) REVERT: A 618 HIS cc_start: 0.6973 (m-70) cc_final: 0.6646 (m-70) REVERT: C 49 TRP cc_start: 0.7906 (m-10) cc_final: 0.7642 (m-10) REVERT: D 37 TYR cc_start: 0.8477 (m-10) cc_final: 0.8203 (m-10) REVERT: D 49 TRP cc_start: 0.7941 (m-10) cc_final: 0.7685 (m-10) REVERT: B 32 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7554 (mt0) REVERT: B 59 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 66 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6168 (mt-10) REVERT: B 80 LYS cc_start: 0.8432 (mttt) cc_final: 0.7802 (mttt) REVERT: B 139 ASN cc_start: 0.7826 (m110) cc_final: 0.7571 (m110) REVERT: B 168 VAL cc_start: 0.8323 (t) cc_final: 0.7937 (p) REVERT: B 171 ASP cc_start: 0.7194 (t0) cc_final: 0.6706 (t0) REVERT: B 172 PHE cc_start: 0.7984 (m-10) cc_final: 0.7451 (m-10) REVERT: B 210 LEU cc_start: 0.8410 (mm) cc_final: 0.7844 (tp) REVERT: B 252 ARG cc_start: 0.7031 (ttt-90) cc_final: 0.6796 (ttp-110) REVERT: B 253 LYS cc_start: 0.8192 (tttm) cc_final: 0.7794 (tttp) REVERT: B 255 ARG cc_start: 0.6944 (mtp85) cc_final: 0.6526 (ttm-80) REVERT: B 261 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7143 (mmtt) REVERT: B 263 THR cc_start: 0.8478 (m) cc_final: 0.8184 (p) REVERT: B 278 ASP cc_start: 0.7374 (m-30) cc_final: 0.6906 (m-30) REVERT: B 286 SER cc_start: 0.7124 (m) cc_final: 0.6842 (m) REVERT: B 293 LYS cc_start: 0.8362 (mttm) cc_final: 0.8131 (mttm) REVERT: B 309 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7654 (mtt180) REVERT: B 350 SER cc_start: 0.6813 (t) cc_final: 0.6602 (p) REVERT: B 364 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8494 (m) REVERT: B 382 THR cc_start: 0.3152 (OUTLIER) cc_final: 0.2866 (m) REVERT: B 396 LYS cc_start: 0.7731 (mttt) cc_final: 0.6746 (mttm) REVERT: B 399 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6659 (mtpp) REVERT: B 415 THR cc_start: 0.7669 (p) cc_final: 0.7144 (t) REVERT: B 427 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7730 (mmt90) REVERT: B 454 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7655 (mmtt) REVERT: B 458 ASP cc_start: 0.7837 (t0) cc_final: 0.7310 (t0) REVERT: B 487 LYS cc_start: 0.7856 (pttp) cc_final: 0.7446 (pttp) REVERT: B 502 THR cc_start: 0.8299 (p) cc_final: 0.8022 (t) REVERT: B 534 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: B 559 HIS cc_start: 0.7617 (t-90) cc_final: 0.7369 (t-90) REVERT: B 561 GLU cc_start: 0.6768 (tp30) cc_final: 0.6452 (tp30) REVERT: B 618 HIS cc_start: 0.6916 (m-70) cc_final: 0.6567 (m90) outliers start: 32 outliers final: 16 residues processed: 314 average time/residue: 0.1246 time to fit residues: 50.5542 Evaluate side-chains 310 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.157836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133225 restraints weight = 15114.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137635 restraints weight = 7686.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140583 restraints weight = 4707.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142639 restraints weight = 3278.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144039 restraints weight = 2501.585| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10340 Z= 0.166 Angle : 0.772 10.553 14036 Z= 0.374 Chirality : 0.050 0.334 1550 Planarity : 0.004 0.032 1814 Dihedral : 7.489 55.669 1620 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.68 % Allowed : 18.12 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.24), residues: 1272 helix: -2.01 (0.69), residues: 52 sheet: -1.94 (0.58), residues: 74 loop : -1.14 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 72 TYR 0.018 0.002 TYR B 117 PHE 0.024 0.002 PHE A 404 TRP 0.042 0.002 TRP C 49 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00366 (10276) covalent geometry : angle 0.73760 (13896) SS BOND : bond 0.00418 ( 52) SS BOND : angle 1.54822 ( 104) hydrogen bonds : bond 0.03643 ( 138) hydrogen bonds : angle 6.27766 ( 252) link_ALPHA1-3 : bond 0.02556 ( 2) link_ALPHA1-3 : angle 3.61725 ( 6) link_BETA1-3 : bond 0.00649 ( 2) link_BETA1-3 : angle 2.94185 ( 6) link_BETA1-4 : bond 0.00810 ( 2) link_BETA1-4 : angle 2.05405 ( 6) link_NAG-ASN : bond 0.00627 ( 6) link_NAG-ASN : angle 4.69692 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7947 (mm110) cc_final: 0.7628 (mt0) REVERT: A 54 MET cc_start: 0.7869 (tpp) cc_final: 0.7070 (tpp) REVERT: A 58 CYS cc_start: 0.5221 (t) cc_final: 0.4966 (t) REVERT: A 59 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 80 LYS cc_start: 0.8367 (mttt) cc_final: 0.7696 (mtmt) REVERT: A 83 GLN cc_start: 0.7252 (mt0) cc_final: 0.6755 (mt0) REVERT: A 171 ASP cc_start: 0.6723 (t0) cc_final: 0.6194 (t0) REVERT: A 172 PHE cc_start: 0.7845 (m-10) cc_final: 0.7275 (m-10) REVERT: A 210 LEU cc_start: 0.8459 (mm) cc_final: 0.8206 (mm) REVERT: A 252 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6688 (ttp-110) REVERT: A 256 ASP cc_start: 0.6613 (m-30) cc_final: 0.6402 (m-30) REVERT: A 340 ILE cc_start: 0.8282 (mp) cc_final: 0.7943 (mt) REVERT: A 357 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7777 (mtmm) REVERT: A 382 THR cc_start: 0.2366 (OUTLIER) cc_final: 0.2111 (m) REVERT: A 399 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6864 (mtpp) REVERT: A 405 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7176 (tp) REVERT: A 454 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7579 (mmtt) REVERT: A 458 ASP cc_start: 0.7859 (t0) cc_final: 0.7293 (t0) REVERT: A 489 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7625 (mtmt) REVERT: A 521 ARG cc_start: 0.7410 (ppt-90) cc_final: 0.6953 (ppt-90) REVERT: A 522 ASP cc_start: 0.6778 (m-30) cc_final: 0.6524 (t0) REVERT: A 586 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6552 (tp) REVERT: A 618 HIS cc_start: 0.7025 (m-70) cc_final: 0.6700 (m-70) REVERT: D 37 TYR cc_start: 0.8488 (m-10) cc_final: 0.8234 (m-80) REVERT: D 49 TRP cc_start: 0.7871 (m-10) cc_final: 0.7624 (m-10) REVERT: B 32 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7619 (mt0) REVERT: B 59 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 66 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6137 (mt-10) REVERT: B 71 GLN cc_start: 0.7697 (mp10) cc_final: 0.7492 (mp10) REVERT: B 80 LYS cc_start: 0.8431 (mttt) cc_final: 0.7822 (mttt) REVERT: B 98 ARG cc_start: 0.7830 (ttt90) cc_final: 0.7424 (mmm-85) REVERT: B 139 ASN cc_start: 0.7846 (m110) cc_final: 0.7626 (m110) REVERT: B 168 VAL cc_start: 0.8392 (t) cc_final: 0.7988 (p) REVERT: B 171 ASP cc_start: 0.7215 (t0) cc_final: 0.6717 (t0) REVERT: B 172 PHE cc_start: 0.7899 (m-10) cc_final: 0.7378 (m-10) REVERT: B 210 LEU cc_start: 0.8412 (mm) cc_final: 0.7837 (tp) REVERT: B 261 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7163 (mmtt) REVERT: B 263 THR cc_start: 0.8467 (m) cc_final: 0.8232 (p) REVERT: B 278 ASP cc_start: 0.7382 (m-30) cc_final: 0.6926 (m-30) REVERT: B 286 SER cc_start: 0.7119 (m) cc_final: 0.6805 (m) REVERT: B 293 LYS cc_start: 0.8359 (mttm) cc_final: 0.8092 (mttm) REVERT: B 350 SER cc_start: 0.6799 (t) cc_final: 0.6586 (p) REVERT: B 364 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8514 (m) REVERT: B 382 THR cc_start: 0.3416 (OUTLIER) cc_final: 0.3141 (m) REVERT: B 399 LYS cc_start: 0.7030 (mtpp) cc_final: 0.6582 (mtpp) REVERT: B 454 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7665 (mmtt) REVERT: B 458 ASP cc_start: 0.7801 (t0) cc_final: 0.7332 (t0) REVERT: B 487 LYS cc_start: 0.7874 (pttp) cc_final: 0.7425 (pttp) REVERT: B 502 THR cc_start: 0.8323 (p) cc_final: 0.8078 (t) REVERT: B 534 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: B 618 HIS cc_start: 0.6919 (m-70) cc_final: 0.6570 (m90) outliers start: 30 outliers final: 19 residues processed: 311 average time/residue: 0.1314 time to fit residues: 52.8026 Evaluate side-chains 318 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 486 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130982 restraints weight = 15173.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135348 restraints weight = 7787.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138263 restraints weight = 4781.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140266 restraints weight = 3321.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141554 restraints weight = 2543.414| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10340 Z= 0.197 Angle : 0.812 10.971 14036 Z= 0.397 Chirality : 0.051 0.331 1550 Planarity : 0.004 0.061 1814 Dihedral : 7.481 55.417 1620 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.77 % Allowed : 18.93 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1272 helix: -1.90 (0.70), residues: 50 sheet: -2.01 (0.57), residues: 74 loop : -1.16 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 72 TYR 0.031 0.002 TYR B 471 PHE 0.022 0.002 PHE A 404 TRP 0.057 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00436 (10276) covalent geometry : angle 0.77808 (13896) SS BOND : bond 0.00418 ( 52) SS BOND : angle 1.59682 ( 104) hydrogen bonds : bond 0.03991 ( 138) hydrogen bonds : angle 6.27534 ( 252) link_ALPHA1-3 : bond 0.02522 ( 2) link_ALPHA1-3 : angle 3.68751 ( 6) link_BETA1-3 : bond 0.00543 ( 2) link_BETA1-3 : angle 2.98623 ( 6) link_BETA1-4 : bond 0.00766 ( 2) link_BETA1-4 : angle 2.06926 ( 6) link_NAG-ASN : bond 0.00725 ( 6) link_NAG-ASN : angle 4.86739 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7955 (mm110) cc_final: 0.7631 (mt0) REVERT: A 54 MET cc_start: 0.7825 (tpp) cc_final: 0.7032 (tpp) REVERT: A 58 CYS cc_start: 0.5260 (t) cc_final: 0.4996 (t) REVERT: A 59 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7156 (mt-10) REVERT: A 80 LYS cc_start: 0.8391 (mttt) cc_final: 0.7709 (mtmt) REVERT: A 83 GLN cc_start: 0.7272 (mt0) cc_final: 0.6774 (mt0) REVERT: A 152 ASN cc_start: 0.7558 (t0) cc_final: 0.7094 (t0) REVERT: A 171 ASP cc_start: 0.6757 (t0) cc_final: 0.6332 (t0) REVERT: A 172 PHE cc_start: 0.7867 (m-10) cc_final: 0.7289 (m-10) REVERT: A 198 SER cc_start: 0.6501 (m) cc_final: 0.6195 (t) REVERT: A 210 LEU cc_start: 0.8483 (mm) cc_final: 0.8225 (mm) REVERT: A 252 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6754 (ttp-110) REVERT: A 340 ILE cc_start: 0.8318 (mp) cc_final: 0.7941 (mt) REVERT: A 357 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 382 THR cc_start: 0.2625 (OUTLIER) cc_final: 0.2361 (m) REVERT: A 399 LYS cc_start: 0.7242 (mtpp) cc_final: 0.6860 (mtpp) REVERT: A 400 GLU cc_start: 0.7425 (tt0) cc_final: 0.7214 (tt0) REVERT: A 405 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7138 (tp) REVERT: A 454 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7590 (mmtt) REVERT: A 458 ASP cc_start: 0.7852 (t0) cc_final: 0.7333 (t0) REVERT: A 521 ARG cc_start: 0.7430 (ppt-90) cc_final: 0.7021 (ppt-90) REVERT: A 586 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6578 (tp) REVERT: A 600 MET cc_start: 0.6236 (tpp) cc_final: 0.5683 (tpp) REVERT: A 618 HIS cc_start: 0.7204 (m-70) cc_final: 0.6929 (m-70) REVERT: C 15 LEU cc_start: 0.7589 (mt) cc_final: 0.7388 (mt) REVERT: C 49 TRP cc_start: 0.7715 (m-10) cc_final: 0.7462 (m-10) REVERT: B 32 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7550 (mt0) REVERT: B 59 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 66 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6152 (mt-10) REVERT: B 80 LYS cc_start: 0.8442 (mttt) cc_final: 0.7817 (mttt) REVERT: B 98 ARG cc_start: 0.7877 (ttt90) cc_final: 0.7496 (mmm-85) REVERT: B 168 VAL cc_start: 0.8332 (t) cc_final: 0.7938 (p) REVERT: B 171 ASP cc_start: 0.7254 (t0) cc_final: 0.6749 (t0) REVERT: B 172 PHE cc_start: 0.7890 (m-10) cc_final: 0.7337 (m-10) REVERT: B 210 LEU cc_start: 0.8417 (mm) cc_final: 0.7848 (tp) REVERT: B 261 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7164 (mmtt) REVERT: B 263 THR cc_start: 0.8412 (m) cc_final: 0.8181 (p) REVERT: B 278 ASP cc_start: 0.7338 (m-30) cc_final: 0.6897 (m-30) REVERT: B 286 SER cc_start: 0.7178 (m) cc_final: 0.6857 (m) REVERT: B 293 LYS cc_start: 0.8360 (mttm) cc_final: 0.8093 (mttm) REVERT: B 350 SER cc_start: 0.6807 (t) cc_final: 0.6605 (p) REVERT: B 364 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 382 THR cc_start: 0.3627 (OUTLIER) cc_final: 0.3353 (m) REVERT: B 399 LYS cc_start: 0.7062 (mtpp) cc_final: 0.6640 (mtpp) REVERT: B 454 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7679 (mmtt) REVERT: B 458 ASP cc_start: 0.7851 (t0) cc_final: 0.7339 (t0) REVERT: B 487 LYS cc_start: 0.7847 (pttp) cc_final: 0.7372 (pttp) REVERT: B 502 THR cc_start: 0.8340 (p) cc_final: 0.8121 (t) REVERT: B 534 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: B 618 HIS cc_start: 0.7004 (m-70) cc_final: 0.6627 (m90) outliers start: 31 outliers final: 20 residues processed: 313 average time/residue: 0.1125 time to fit residues: 46.7012 Evaluate side-chains 325 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain D residue 33 CYS Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128798 restraints weight = 15087.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133049 restraints weight = 7735.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135950 restraints weight = 4759.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137936 restraints weight = 3303.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139324 restraints weight = 2520.701| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10340 Z= 0.252 Angle : 0.856 10.847 14036 Z= 0.422 Chirality : 0.053 0.331 1550 Planarity : 0.005 0.058 1814 Dihedral : 7.635 54.969 1620 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.95 % Allowed : 19.20 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.23), residues: 1272 helix: -2.08 (0.67), residues: 50 sheet: -2.01 (0.57), residues: 74 loop : -1.21 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.026 0.002 TYR B 117 PHE 0.038 0.003 PHE B 404 TRP 0.053 0.003 TRP C 49 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00542 (10276) covalent geometry : angle 0.82018 (13896) SS BOND : bond 0.00481 ( 52) SS BOND : angle 1.64619 ( 104) hydrogen bonds : bond 0.04269 ( 138) hydrogen bonds : angle 6.40680 ( 252) link_ALPHA1-3 : bond 0.02324 ( 2) link_ALPHA1-3 : angle 3.66966 ( 6) link_BETA1-3 : bond 0.00309 ( 2) link_BETA1-3 : angle 3.02365 ( 6) link_BETA1-4 : bond 0.00570 ( 2) link_BETA1-4 : angle 2.19941 ( 6) link_NAG-ASN : bond 0.00976 ( 6) link_NAG-ASN : angle 5.24157 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7972 (mm110) cc_final: 0.7653 (mt0) REVERT: A 54 MET cc_start: 0.7803 (tpp) cc_final: 0.7282 (tpp) REVERT: A 58 CYS cc_start: 0.5270 (t) cc_final: 0.5039 (t) REVERT: A 59 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 80 LYS cc_start: 0.8394 (mttt) cc_final: 0.7736 (mtmt) REVERT: A 83 GLN cc_start: 0.7307 (mt0) cc_final: 0.6811 (mt0) REVERT: A 152 ASN cc_start: 0.7533 (t0) cc_final: 0.7217 (t0) REVERT: A 171 ASP cc_start: 0.6949 (t0) cc_final: 0.6497 (t0) REVERT: A 172 PHE cc_start: 0.7845 (m-10) cc_final: 0.7290 (m-10) REVERT: A 198 SER cc_start: 0.6621 (m) cc_final: 0.6410 (t) REVERT: A 210 LEU cc_start: 0.8407 (mm) cc_final: 0.8144 (mm) REVERT: A 252 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6745 (ttp-110) REVERT: A 260 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.5068 (m) REVERT: A 340 ILE cc_start: 0.8298 (mp) cc_final: 0.8040 (mt) REVERT: A 357 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7768 (mtmm) REVERT: A 360 LYS cc_start: 0.8070 (tppp) cc_final: 0.7845 (tptp) REVERT: A 382 THR cc_start: 0.3000 (OUTLIER) cc_final: 0.2724 (m) REVERT: A 396 LYS cc_start: 0.7855 (mttt) cc_final: 0.7206 (mttm) REVERT: A 399 LYS cc_start: 0.7310 (mtpp) cc_final: 0.6829 (mtpp) REVERT: A 400 GLU cc_start: 0.7429 (tt0) cc_final: 0.7217 (tt0) REVERT: A 405 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7116 (tp) REVERT: A 410 TRP cc_start: 0.6855 (OUTLIER) cc_final: 0.6192 (m-90) REVERT: A 454 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7475 (mmtt) REVERT: A 458 ASP cc_start: 0.7915 (t0) cc_final: 0.7396 (t0) REVERT: A 521 ARG cc_start: 0.7439 (ppt-90) cc_final: 0.7081 (ppt-90) REVERT: A 600 MET cc_start: 0.6271 (tpp) cc_final: 0.5742 (tpp) REVERT: A 618 HIS cc_start: 0.7096 (m-70) cc_final: 0.6681 (m170) REVERT: C 49 TRP cc_start: 0.7653 (m-10) cc_final: 0.7428 (m-10) REVERT: B 29 LYS cc_start: 0.7189 (mttp) cc_final: 0.6951 (mttp) REVERT: B 32 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7454 (mt0) REVERT: B 59 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 66 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6123 (mt-10) REVERT: B 80 LYS cc_start: 0.8467 (mttt) cc_final: 0.7817 (mttt) REVERT: B 98 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7504 (mmm-85) REVERT: B 168 VAL cc_start: 0.8394 (t) cc_final: 0.7994 (p) REVERT: B 171 ASP cc_start: 0.7331 (t0) cc_final: 0.7058 (t0) REVERT: B 210 LEU cc_start: 0.8367 (mm) cc_final: 0.7907 (tp) REVERT: B 261 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7201 (mmtt) REVERT: B 263 THR cc_start: 0.8421 (m) cc_final: 0.8177 (p) REVERT: B 278 ASP cc_start: 0.7305 (m-30) cc_final: 0.6900 (m-30) REVERT: B 286 SER cc_start: 0.7314 (m) cc_final: 0.6967 (m) REVERT: B 293 LYS cc_start: 0.8369 (mttm) cc_final: 0.8097 (mttm) REVERT: B 364 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8529 (m) REVERT: B 382 THR cc_start: 0.4047 (OUTLIER) cc_final: 0.3774 (m) REVERT: B 399 LYS cc_start: 0.7144 (mtpp) cc_final: 0.6730 (mtpp) REVERT: B 454 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7675 (mmtt) REVERT: B 458 ASP cc_start: 0.7921 (t0) cc_final: 0.7496 (t0) REVERT: B 487 LYS cc_start: 0.7919 (pttp) cc_final: 0.7438 (pttp) REVERT: B 502 THR cc_start: 0.8415 (p) cc_final: 0.8214 (t) REVERT: B 618 HIS cc_start: 0.7208 (m-70) cc_final: 0.6830 (m90) outliers start: 33 outliers final: 21 residues processed: 315 average time/residue: 0.1190 time to fit residues: 49.1478 Evaluate side-chains 332 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 117 optimal weight: 0.0270 chunk 64 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130077 restraints weight = 15190.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134464 restraints weight = 7755.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137421 restraints weight = 4734.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139413 restraints weight = 3269.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140704 restraints weight = 2487.419| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10340 Z= 0.182 Angle : 0.837 10.148 14036 Z= 0.410 Chirality : 0.051 0.347 1550 Planarity : 0.005 0.051 1814 Dihedral : 7.390 54.960 1620 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.41 % Allowed : 20.18 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1272 helix: -2.13 (0.66), residues: 50 sheet: -1.88 (0.57), residues: 74 loop : -1.15 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 149 TYR 0.029 0.002 TYR B 471 PHE 0.032 0.002 PHE B 404 TRP 0.065 0.003 TRP D 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00403 (10276) covalent geometry : angle 0.80212 (13896) SS BOND : bond 0.00417 ( 52) SS BOND : angle 1.62341 ( 104) hydrogen bonds : bond 0.03982 ( 138) hydrogen bonds : angle 6.29225 ( 252) link_ALPHA1-3 : bond 0.02558 ( 2) link_ALPHA1-3 : angle 3.88398 ( 6) link_BETA1-3 : bond 0.00609 ( 2) link_BETA1-3 : angle 3.12887 ( 6) link_BETA1-4 : bond 0.00838 ( 2) link_BETA1-4 : angle 2.29823 ( 6) link_NAG-ASN : bond 0.00669 ( 6) link_NAG-ASN : angle 4.96797 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.27 seconds wall clock time: 33 minutes 36.71 seconds (2016.71 seconds total)