Starting phenix.real_space_refine on Sat Jul 4 04:06:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hgs_34746/07_2026/8hgs_34746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgs_34746/07_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_34746/07_2026/8hgs_34746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgs_34746/07_2026/8hgs_34746.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hgs_34746/07_2026/8hgs_34746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hgs_34746/07_2026/8hgs_34746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgs_34746/07_2026/8hgs_34746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgs_34746/07_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-6108/lib/python3.11/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 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 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 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 chiralities: 2 Time building chain proxies: 2.06, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 410.6 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: 1.27 Time building geometry restraints manager: 1.16 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 - 14.41: 5960 14.41 - 28.82: 220 28.82 - 43.24: 82 43.24 - 57.65: 18 57.65 - 72.06: 12 Dihedral angle restraints: 6292 sinusoidal: 2616 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 6289 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: 0.01 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 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 : 8.447 70.668 3776 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/Z covalent geometry : bond 0.00394 / 0.20 (10276) covalent geometry : angle 0.74831 / 0.40 (13896) SS BOND : bond 0.00330 / 0.20 ( 52) SS BOND : angle 1.08813 / 0.72 ( 104) hydrogen bonds : bond 0.21724 / 13.61 ( 138) hydrogen bonds : angle 6.98730 / 4.84 ( 252) link_ALPHA1-3 : bond 0.01502 / 0.75 ( 2) link_ALPHA1-3 : angle 2.28169 / 1.24 ( 6) link_BETA1-3 : bond 0.01574 / 0.79 ( 2) link_BETA1-3 : angle 7.29947 / 4.06 ( 6) link_BETA1-4 : bond 0.01613 / 0.81 ( 2) link_BETA1-4 : angle 1.91480 / 0.95 ( 6) link_NAG-ASN : bond 0.01039 / 0.64 ( 6) link_NAG-ASN : angle 4.99238 / 2.46 ( 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 : 0.435 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: 0.1333 time to fit residues: 57.0822 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 : 0.381 ------------------------------------------------------------------------------- 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... 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 = 0.4225 r_free = 0.4225 target = 0.174734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150433 restraints weight = 15514.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155025 restraints weight = 7889.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158054 restraints weight = 4825.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160107 restraints weight = 3355.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.161380 restraints weight = 2571.808| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 10340 Z= 0.210 Angle : 0.753 13.196 14036 Z= 0.377 Chirality : 0.052 0.297 1550 Planarity : 0.005 0.065 1814 Dihedral : 5.748 35.230 1376 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.05 % Allowed : 8.30 % Favored : 89.64 % 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: -2.56 (0.21), residues: 1272 helix: -0.61 (0.90), residues: 40 sheet: -2.49 (0.45), residues: 84 loop : -1.88 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 252 TYR 0.014 0.002 TYR D 37 PHE 0.022 0.002 PHE B 180 TRP 0.005 0.001 TRP B 410 HIS 0.006 0.002 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (10276) covalent geometry : angle 0.71404 / 0.36 (13896) SS BOND : bond 0.00787 / 0.47 ( 52) SS BOND : angle 2.11493 / 1.42 ( 104) hydrogen bonds : bond 0.04092 / 2.73 ( 138) hydrogen bonds : angle 6.21017 / 4.30 ( 252) link_ALPHA1-3 : bond 0.00733 / 0.35 ( 2) link_ALPHA1-3 : angle 1.64502 / 0.77 ( 6) link_BETA1-3 : bond 0.00605 / 0.29 ( 2) link_BETA1-3 : angle 3.85360 / 2.08 ( 6) link_BETA1-4 : bond 0.00303 / 0.14 ( 2) link_BETA1-4 : angle 0.62170 / 0.32 ( 6) link_NAG-ASN : bond 0.00655 / 0.38 ( 6) link_NAG-ASN : angle 4.06711 / 2.01 ( 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 318 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.409 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 37 LYS cc_start: 0.8156 (mttt) cc_final: 0.7917 (mttp) REVERT: A 46 ASP cc_start: 0.7290 (m-30) cc_final: 0.6801 (m-30) REVERT: A 54 MET cc_start: 0.7506 (tpp) cc_final: 0.7231 (tpp) REVERT: A 58 CYS cc_start: 0.5271 (t) cc_final: 0.5044 (t) REVERT: A 64 ASN cc_start: 0.8158 (m-40) cc_final: 0.7826 (m-40) REVERT: A 80 LYS cc_start: 0.7944 (mttt) cc_final: 0.7531 (mtmt) REVERT: A 83 GLN cc_start: 0.7463 (mt0) cc_final: 0.6793 (mt0) REVERT: A 105 GLN cc_start: 0.8043 (mt0) cc_final: 0.7685 (mt0) REVERT: A 108 ARG cc_start: 0.7572 (mtt-85) cc_final: 0.7122 (mmm-85) REVERT: A 139 ASN cc_start: 0.8023 (m110) cc_final: 0.7625 (m-40) REVERT: A 222 ARG cc_start: 0.5199 (mtt-85) cc_final: 0.4793 (mtp85) REVERT: A 246 SER cc_start: 0.8267 (p) cc_final: 0.8056 (m) REVERT: A 253 LYS cc_start: 0.8040 (mttp) cc_final: 0.7712 (mttp) REVERT: A 255 ARG cc_start: 0.6996 (ttm-80) cc_final: 0.6731 (ttt-90) REVERT: A 268 MET cc_start: 0.7127 (mmt) cc_final: 0.6832 (mmt) REVERT: A 340 ILE cc_start: 0.8102 (mp) cc_final: 0.7743 (mt) REVERT: A 350 SER cc_start: 0.6822 (t) cc_final: 0.6494 (p) REVERT: A 399 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6465 (mtpp) REVERT: A 405 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7094 (tp) REVERT: A 422 ASN cc_start: 0.7841 (m-40) cc_final: 0.7450 (m-40) REVERT: A 436 PHE cc_start: 0.7490 (m-80) cc_final: 0.7236 (m-80) REVERT: A 451 ARG cc_start: 0.6974 (ptp90) cc_final: 0.5700 (ptp90) REVERT: A 452 SER cc_start: 0.6992 (p) cc_final: 0.6764 (t) REVERT: A 521 ARG cc_start: 0.6980 (ppt-90) cc_final: 0.6543 (ppt-90) REVERT: A 548 GLU cc_start: 0.4906 (mp0) cc_final: 0.4411 (mp0) REVERT: A 559 HIS cc_start: 0.6687 (t-90) cc_final: 0.6430 (t-90) REVERT: A 574 ARG cc_start: 0.7255 (ptp90) cc_final: 0.6847 (mpp-170) REVERT: A 618 HIS cc_start: 0.6431 (m-70) cc_final: 0.6178 (m-70) REVERT: B 32 GLN cc_start: 0.7790 (mm110) cc_final: 0.7519 (mt0) REVERT: B 59 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 80 LYS cc_start: 0.8268 (mttt) cc_final: 0.7751 (mttt) REVERT: B 149 ARG cc_start: 0.7031 (ttt90) cc_final: 0.6805 (ttt90) REVERT: B 168 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 171 ASP cc_start: 0.6821 (t0) cc_final: 0.6521 (t0) REVERT: B 253 LYS cc_start: 0.8044 (mttp) cc_final: 0.7720 (mttp) REVERT: B 278 ASP cc_start: 0.7112 (m-30) cc_final: 0.6668 (m-30) REVERT: B 321 ASP cc_start: 0.6014 (m-30) cc_final: 0.5242 (m-30) REVERT: B 345 PHE cc_start: 0.7527 (m-10) cc_final: 0.7083 (m-10) REVERT: B 364 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (m) REVERT: B 369 LEU cc_start: 0.8259 (mt) cc_final: 0.7883 (mt) REVERT: B 399 LYS cc_start: 0.6952 (mtpp) cc_final: 0.6431 (mtpp) REVERT: B 400 GLU cc_start: 0.7143 (tt0) cc_final: 0.6883 (tt0) REVERT: B 452 SER cc_start: 0.6732 (p) cc_final: 0.5739 (p) REVERT: B 454 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7600 (mmtt) REVERT: B 458 ASP cc_start: 0.7663 (t0) cc_final: 0.7049 (t0) REVERT: B 460 ASP cc_start: 0.6302 (m-30) cc_final: 0.5790 (m-30) REVERT: B 475 ILE cc_start: 0.6735 (mm) cc_final: 0.6516 (mp) REVERT: B 487 LYS cc_start: 0.7150 (pttp) cc_final: 0.6535 (pttp) REVERT: B 521 ARG cc_start: 0.6864 (ppt-90) cc_final: 0.6561 (ppt-90) REVERT: B 618 HIS cc_start: 0.6508 (m-70) cc_final: 0.6305 (m90) outliers start: 23 outliers final: 10 residues processed: 306 average time/residue: 0.1354 time to fit residues: 54.4701 Evaluate side-chains 293 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 364 SER 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: 0.9980 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 206 ASN A 235 GLN A 408 GLN A 444 ASN A 493 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN C 10 HIS C 16 HIS D 10 HIS B 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN B 559 HIS B 568 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.162781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137640 restraints weight = 15082.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.142098 restraints weight = 7710.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145036 restraints weight = 4753.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147053 restraints weight = 3341.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148491 restraints weight = 2575.464| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10340 Z= 0.263 Angle : 0.811 9.661 14036 Z= 0.413 Chirality : 0.054 0.336 1550 Planarity : 0.005 0.096 1814 Dihedral : 6.209 54.641 1376 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.41 % Allowed : 10.45 % Favored : 87.14 % 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: -2.17 (0.22), residues: 1272 helix: -0.48 (0.94), residues: 42 sheet: -2.54 (0.53), residues: 64 loop : -1.58 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 533 TYR 0.023 0.002 TYR A 125 PHE 0.018 0.003 PHE A 78 TRP 0.018 0.002 TRP C 49 HIS 0.008 0.002 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (10276) covalent geometry : angle 0.78434 / 0.41 (13896) SS BOND : bond 0.00808 / 0.47 ( 52) SS BOND : angle 1.70559 / 1.14 ( 104) hydrogen bonds : bond 0.04236 / 2.76 ( 138) hydrogen bonds : angle 6.54625 / 4.43 ( 252) link_ALPHA1-3 : bond 0.00794 / 0.40 ( 2) link_ALPHA1-3 : angle 1.49044 / 0.75 ( 6) link_BETA1-3 : bond 0.00488 / 0.24 ( 2) link_BETA1-3 : angle 2.89946 / 1.55 ( 6) link_BETA1-4 : bond 0.00466 / 0.23 ( 2) link_BETA1-4 : angle 1.40888 / 0.70 ( 6) link_NAG-ASN : bond 0.00895 / 0.43 ( 6) link_NAG-ASN : angle 4.10987 / 2.02 ( 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 341 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 0.363 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: 0.8189 (mm110) cc_final: 0.7945 (mp10) REVERT: A 37 LYS cc_start: 0.8175 (mttt) cc_final: 0.7873 (mttm) REVERT: A 46 ASP cc_start: 0.7338 (m-30) cc_final: 0.6854 (m-30) REVERT: A 58 CYS cc_start: 0.5327 (t) cc_final: 0.5100 (t) REVERT: A 59 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 64 ASN cc_start: 0.8270 (m-40) cc_final: 0.7672 (m-40) REVERT: A 80 LYS cc_start: 0.8218 (mttt) cc_final: 0.7594 (mmtt) REVERT: A 105 GLN cc_start: 0.8247 (mt0) cc_final: 0.7946 (mt0) REVERT: A 111 MET cc_start: 0.7271 (ptm) cc_final: 0.7065 (ptm) REVERT: A 139 ASN cc_start: 0.8193 (m110) cc_final: 0.7945 (m-40) REVERT: A 149 ARG cc_start: 0.6815 (ttt-90) cc_final: 0.6612 (ttt-90) REVERT: A 152 ASN cc_start: 0.7207 (t0) cc_final: 0.6869 (t0) REVERT: A 222 ARG cc_start: 0.5857 (mtt-85) cc_final: 0.5285 (mtt90) REVERT: A 235 GLN cc_start: 0.7409 (mm110) cc_final: 0.6977 (mm-40) REVERT: A 252 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7140 (ttp-110) REVERT: A 254 PHE cc_start: 0.7764 (m-10) cc_final: 0.7559 (m-80) REVERT: A 263 THR cc_start: 0.8476 (p) cc_final: 0.8264 (p) REVERT: A 299 TYR cc_start: 0.7974 (m-80) cc_final: 0.7457 (m-80) REVERT: A 335 LYS cc_start: 0.7600 (tptp) cc_final: 0.7283 (tptp) REVERT: A 340 ILE cc_start: 0.8411 (mp) cc_final: 0.8040 (mt) REVERT: A 350 SER cc_start: 0.6900 (t) cc_final: 0.6671 (p) REVERT: A 357 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7750 (mtmm) REVERT: A 399 LYS cc_start: 0.7232 (mtpp) cc_final: 0.6875 (mtpp) REVERT: A 405 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6876 (tp) REVERT: A 426 ILE cc_start: 0.8035 (mt) cc_final: 0.7416 (tt) REVERT: A 451 ARG cc_start: 0.7307 (ptp90) cc_final: 0.6321 (ptp90) REVERT: A 452 SER cc_start: 0.7217 (p) cc_final: 0.6085 (t) REVERT: A 454 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7635 (mmtt) REVERT: A 458 ASP cc_start: 0.7725 (t0) cc_final: 0.7208 (t0) REVERT: A 460 ASP cc_start: 0.6407 (m-30) cc_final: 0.6168 (m-30) REVERT: A 521 ARG cc_start: 0.7136 (ppt-90) cc_final: 0.6833 (ppt-90) REVERT: A 533 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6799 (mmm-85) REVERT: A 548 GLU cc_start: 0.5195 (mp0) cc_final: 0.4955 (mp0) REVERT: A 561 GLU cc_start: 0.6276 (tp30) cc_final: 0.3493 (mm-30) REVERT: A 618 HIS cc_start: 0.6920 (m-70) cc_final: 0.6439 (m170) REVERT: B 54 MET cc_start: 0.8178 (tpp) cc_final: 0.7325 (tpp) REVERT: B 59 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 66 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 80 LYS cc_start: 0.8368 (mttt) cc_final: 0.7775 (mttt) REVERT: B 112 TYR cc_start: 0.7641 (m-80) cc_final: 0.6623 (m-80) REVERT: B 128 ASN cc_start: 0.7384 (p0) cc_final: 0.7166 (p0) REVERT: B 168 VAL cc_start: 0.8408 (t) cc_final: 0.8056 (p) REVERT: B 171 ASP cc_start: 0.7050 (t0) cc_final: 0.6622 (t0) REVERT: B 235 GLN cc_start: 0.7580 (mp10) cc_final: 0.6473 (mm-40) REVERT: B 271 ASN cc_start: 0.7971 (t0) cc_final: 0.7296 (m-40) REVERT: B 278 ASP cc_start: 0.7221 (m-30) cc_final: 0.6061 (m-30) REVERT: B 285 TYR cc_start: 0.7528 (m-80) cc_final: 0.7283 (m-80) REVERT: B 286 SER cc_start: 0.7053 (m) cc_final: 0.6624 (m) REVERT: B 364 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8498 (m) REVERT: B 374 VAL cc_start: 0.8138 (m) cc_final: 0.7803 (t) REVERT: B 382 THR cc_start: 0.2130 (OUTLIER) cc_final: 0.1883 (m) REVERT: B 396 LYS cc_start: 0.7743 (mttt) cc_final: 0.7105 (mttm) REVERT: B 399 LYS cc_start: 0.7091 (mtpp) cc_final: 0.6639 (mtpp) REVERT: B 400 GLU cc_start: 0.7134 (tt0) cc_final: 0.6854 (tt0) REVERT: B 415 THR cc_start: 0.7572 (p) cc_final: 0.7276 (t) REVERT: B 427 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7856 (mmt90) REVERT: B 451 ARG cc_start: 0.7531 (ptp90) cc_final: 0.6127 (ptp90) REVERT: B 454 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7654 (mmtt) REVERT: B 460 ASP cc_start: 0.6408 (m-30) cc_final: 0.6191 (m-30) REVERT: B 487 LYS cc_start: 0.7565 (pttp) cc_final: 0.6957 (pttp) REVERT: B 502 THR cc_start: 0.8074 (p) cc_final: 0.7799 (t) REVERT: B 559 HIS cc_start: 0.7185 (t-90) cc_final: 0.6673 (t-90) REVERT: B 618 HIS cc_start: 0.7138 (m-70) cc_final: 0.6696 (m90) outliers start: 27 outliers final: 12 residues processed: 322 average time/residue: 0.1311 time to fit residues: 55.6146 Evaluate side-chains 305 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 LEU 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: 0.6980 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 361 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 466 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134920 restraints weight = 15247.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139284 restraints weight = 7675.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142204 restraints weight = 4672.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.144197 restraints weight = 3235.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145585 restraints weight = 2462.281| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 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 = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10340 Z= 0.219 Angle : 0.786 15.115 14036 Z= 0.390 Chirality : 0.052 0.334 1550 Planarity : 0.004 0.049 1814 Dihedral : 6.298 48.001 1376 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.59 % Allowed : 13.66 % Favored : 83.75 % 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: -2.09 (0.22), residues: 1272 helix: -0.64 (0.91), residues: 40 sheet: -2.35 (0.54), residues: 78 loop : -1.50 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 149 TYR 0.014 0.002 TYR A 471 PHE 0.028 0.002 PHE B 404 TRP 0.016 0.001 TRP D 49 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (10276) covalent geometry : angle 0.74796 / 0.38 (13896) SS BOND : bond 0.00435 / 0.24 ( 52) SS BOND : angle 2.24098 / 1.30 ( 104) hydrogen bonds : bond 0.03845 / 2.48 ( 138) hydrogen bonds : angle 6.51765 / 4.38 ( 252) link_ALPHA1-3 : bond 0.01044 / 0.53 ( 2) link_ALPHA1-3 : angle 1.14311 / 0.56 ( 6) link_BETA1-3 : bond 0.00993 / 0.50 ( 2) link_BETA1-3 : angle 3.01403 / 1.63 ( 6) link_BETA1-4 : bond 0.00523 / 0.25 ( 2) link_BETA1-4 : angle 1.51235 / 0.77 ( 6) link_NAG-ASN : bond 0.00770 / 0.38 ( 6) link_NAG-ASN : angle 4.07192 / 2.01 ( 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 324 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8157 (mm110) cc_final: 0.7548 (mt0) REVERT: A 37 LYS cc_start: 0.8131 (mttt) cc_final: 0.7901 (mttp) REVERT: A 46 ASP cc_start: 0.7298 (m-30) cc_final: 0.6882 (m-30) REVERT: A 58 CYS cc_start: 0.5260 (t) cc_final: 0.5006 (t) REVERT: A 59 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7061 (mt-10) REVERT: A 64 ASN cc_start: 0.8308 (m-40) cc_final: 0.7631 (m-40) REVERT: A 66 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6366 (mt-10) REVERT: A 80 LYS cc_start: 0.8293 (mttt) cc_final: 0.7660 (mttt) REVERT: A 83 GLN cc_start: 0.7286 (mt0) cc_final: 0.6787 (mt0) REVERT: A 210 LEU cc_start: 0.8405 (mm) cc_final: 0.8148 (mm) REVERT: A 222 ARG cc_start: 0.5952 (mtt-85) cc_final: 0.5626 (mtt90) REVERT: A 235 GLN cc_start: 0.7314 (mm110) cc_final: 0.6901 (mm-40) REVERT: A 252 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7103 (ttp80) REVERT: A 253 LYS cc_start: 0.8193 (mttp) cc_final: 0.7176 (mttp) REVERT: A 297 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6722 (mtp85) REVERT: A 335 LYS cc_start: 0.7594 (tptp) cc_final: 0.7344 (tptp) REVERT: A 340 ILE cc_start: 0.8321 (mp) cc_final: 0.7948 (mt) REVERT: A 357 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7797 (mtmm) REVERT: A 382 THR cc_start: 0.1343 (OUTLIER) cc_final: 0.1129 (m) REVERT: A 399 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6775 (mtpp) REVERT: A 405 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6920 (tp) REVERT: A 426 ILE cc_start: 0.8069 (mt) cc_final: 0.7419 (tt) REVERT: A 451 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6160 (ptp90) REVERT: A 452 SER cc_start: 0.7337 (p) cc_final: 0.6176 (t) REVERT: A 454 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7635 (mmtt) REVERT: A 458 ASP cc_start: 0.7764 (t0) cc_final: 0.7305 (t0) REVERT: A 460 ASP cc_start: 0.6416 (m-30) cc_final: 0.6171 (m-30) REVERT: A 489 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7659 (mtmt) REVERT: A 521 ARG cc_start: 0.7322 (ppt-90) cc_final: 0.6838 (ppt-90) REVERT: A 548 GLU cc_start: 0.3850 (mp0) cc_final: 0.2714 (mp0) REVERT: A 618 HIS cc_start: 0.7125 (m-70) cc_final: 0.6636 (m-70) REVERT: C 44 TYR cc_start: 0.7364 (m-10) cc_final: 0.7085 (m-10) REVERT: B 32 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7554 (mt0) REVERT: B 54 MET cc_start: 0.8068 (tpp) cc_final: 0.7590 (tpp) REVERT: B 59 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 66 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6565 (mt-10) REVERT: B 80 LYS cc_start: 0.8383 (mttt) cc_final: 0.7782 (mttt) REVERT: B 98 ARG cc_start: 0.7523 (ttt90) cc_final: 0.7194 (mtp85) REVERT: B 111 MET cc_start: 0.7018 (ptm) cc_final: 0.6812 (ptm) REVERT: B 168 VAL cc_start: 0.8260 (t) cc_final: 0.7946 (p) REVERT: B 171 ASP cc_start: 0.7050 (t0) cc_final: 0.6512 (t0) REVERT: B 172 PHE cc_start: 0.8112 (m-10) cc_final: 0.7434 (m-10) REVERT: B 235 GLN cc_start: 0.7588 (mp10) cc_final: 0.6775 (mm110) REVERT: B 260 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.4766 (m) REVERT: B 261 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7036 (mmtt) REVERT: B 263 THR cc_start: 0.8495 (m) cc_final: 0.8169 (p) REVERT: B 271 ASN cc_start: 0.7934 (t0) cc_final: 0.7431 (m-40) REVERT: B 286 SER cc_start: 0.7180 (m) cc_final: 0.6888 (m) REVERT: B 345 PHE cc_start: 0.8013 (m-10) cc_final: 0.7697 (m-10) REVERT: B 364 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8520 (m) REVERT: B 369 LEU cc_start: 0.8363 (mt) cc_final: 0.8101 (mt) REVERT: B 374 VAL cc_start: 0.8120 (m) cc_final: 0.7862 (t) REVERT: B 382 THR cc_start: 0.2602 (OUTLIER) cc_final: 0.2323 (m) REVERT: B 396 LYS cc_start: 0.7742 (mttt) cc_final: 0.7122 (mttm) REVERT: B 399 LYS cc_start: 0.7082 (mtpp) cc_final: 0.6647 (mtpp) REVERT: B 404 PHE cc_start: 0.8029 (p90) cc_final: 0.7687 (p90) REVERT: B 415 THR cc_start: 0.7613 (p) cc_final: 0.7205 (t) REVERT: B 454 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7662 (mmtt) REVERT: B 458 ASP cc_start: 0.7820 (t0) cc_final: 0.7135 (t0) REVERT: B 487 LYS cc_start: 0.7697 (pttp) cc_final: 0.7298 (pttp) REVERT: B 502 THR cc_start: 0.8131 (p) cc_final: 0.7837 (t) REVERT: B 559 HIS cc_start: 0.7201 (t-90) cc_final: 0.6895 (t-90) REVERT: B 581 GLN cc_start: 0.7676 (tt0) cc_final: 0.7270 (tm-30) REVERT: B 618 HIS cc_start: 0.7130 (m-70) cc_final: 0.6764 (m90) outliers start: 29 outliers final: 17 residues processed: 306 average time/residue: 0.1375 time to fit residues: 55.0780 Evaluate side-chains 301 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 304 HIS 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 552 ASN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS 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 610 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 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 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 = 0.4019 r_free = 0.4019 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131987 restraints weight = 15301.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136358 restraints weight = 7765.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139313 restraints weight = 4768.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141320 restraints weight = 3319.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142743 restraints weight = 2537.595| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10340 Z= 0.217 Angle : 0.767 9.999 14036 Z= 0.385 Chirality : 0.052 0.343 1550 Planarity : 0.005 0.060 1814 Dihedral : 6.207 46.993 1376 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.95 % Allowed : 14.38 % Favored : 82.68 % Cbeta Deviations : 0.08 % 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: -1.89 (0.23), residues: 1272 helix: -0.97 (0.86), residues: 40 sheet: -2.11 (0.66), residues: 54 loop : -1.37 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.021 0.002 TYR C 37 PHE 0.022 0.002 PHE A 172 TRP 0.038 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (10276) covalent geometry : angle 0.73664 / 0.38 (13896) SS BOND : bond 0.00480 / 0.29 ( 52) SS BOND : angle 1.80223 / 1.08 ( 104) hydrogen bonds : bond 0.03936 / 2.54 ( 138) hydrogen bonds : angle 6.40732 / 4.31 ( 252) link_ALPHA1-3 : bond 0.00607 / 0.30 ( 2) link_ALPHA1-3 : angle 1.48448 / 0.75 ( 6) link_BETA1-3 : bond 0.00326 / 0.16 ( 2) link_BETA1-3 : angle 2.84384 / 1.53 ( 6) link_BETA1-4 : bond 0.00569 / 0.28 ( 2) link_BETA1-4 : angle 1.64328 / 0.83 ( 6) link_NAG-ASN : bond 0.00808 / 0.39 ( 6) link_NAG-ASN : angle 4.09800 / 2.02 ( 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 330 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.383 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: 0.8086 (mm110) cc_final: 0.7569 (mt0) REVERT: A 37 LYS cc_start: 0.8052 (mttt) cc_final: 0.7791 (mttp) REVERT: A 54 MET cc_start: 0.7870 (tpp) cc_final: 0.7509 (tpp) REVERT: A 58 CYS cc_start: 0.5274 (t) cc_final: 0.4994 (t) REVERT: A 59 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 64 ASN cc_start: 0.8274 (m-40) cc_final: 0.7785 (m-40) REVERT: A 66 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6121 (mt-10) REVERT: A 80 LYS cc_start: 0.8355 (mttt) cc_final: 0.7682 (mttt) REVERT: A 83 GLN cc_start: 0.7325 (mt0) cc_final: 0.6766 (mt0) REVERT: A 125 TYR cc_start: 0.7910 (p90) cc_final: 0.7484 (p90) REVERT: A 149 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6826 (mmm-85) REVERT: A 171 ASP cc_start: 0.6571 (t0) cc_final: 0.6127 (t0) REVERT: A 172 PHE cc_start: 0.7915 (m-10) cc_final: 0.7221 (m-10) REVERT: A 210 LEU cc_start: 0.8445 (mm) cc_final: 0.8184 (mm) REVERT: A 235 GLN cc_start: 0.7306 (mm110) cc_final: 0.6949 (mm-40) REVERT: A 252 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7124 (ttp80) REVERT: A 256 ASP cc_start: 0.6687 (m-30) cc_final: 0.6474 (m-30) REVERT: A 260 CYS cc_start: 0.6145 (OUTLIER) cc_final: 0.4734 (m) REVERT: A 299 TYR cc_start: 0.7916 (m-80) cc_final: 0.7468 (m-80) REVERT: A 335 LYS cc_start: 0.7605 (tptp) cc_final: 0.7375 (tptp) REVERT: A 340 ILE cc_start: 0.8349 (mp) cc_final: 0.7980 (mt) REVERT: A 357 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7791 (mtmm) REVERT: A 361 ASN cc_start: 0.7378 (t0) cc_final: 0.7097 (t0) REVERT: A 382 THR cc_start: 0.1712 (OUTLIER) cc_final: 0.1491 (m) REVERT: A 399 LYS cc_start: 0.7145 (mtpp) cc_final: 0.6770 (mtpp) REVERT: A 405 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7112 (tp) REVERT: A 426 ILE cc_start: 0.8094 (mt) cc_final: 0.7511 (tt) REVERT: A 451 ARG cc_start: 0.7403 (ptp90) cc_final: 0.6314 (ptp90) REVERT: A 452 SER cc_start: 0.7475 (p) cc_final: 0.6263 (t) REVERT: A 454 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7627 (mmtt) REVERT: A 458 ASP cc_start: 0.7961 (t0) cc_final: 0.7404 (t0) REVERT: A 460 ASP cc_start: 0.6491 (m-30) cc_final: 0.6003 (m-30) REVERT: A 521 ARG cc_start: 0.7407 (ppt-90) cc_final: 0.6925 (ppt-90) REVERT: A 548 GLU cc_start: 0.3592 (mp0) cc_final: 0.2949 (mp0) REVERT: A 618 HIS cc_start: 0.7034 (m-70) cc_final: 0.6455 (m170) REVERT: D 15 LEU cc_start: 0.8399 (mm) cc_final: 0.8057 (mt) REVERT: D 37 TYR cc_start: 0.8279 (m-80) cc_final: 0.7974 (m-10) REVERT: B 32 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7489 (mt0) REVERT: B 54 MET cc_start: 0.8047 (tpp) cc_final: 0.7677 (tpp) REVERT: B 59 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 66 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6423 (mt-10) REVERT: B 80 LYS cc_start: 0.8418 (mttt) cc_final: 0.7782 (mttt) REVERT: B 98 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7336 (mtp-110) REVERT: B 139 ASN cc_start: 0.7859 (m110) cc_final: 0.7570 (m-40) REVERT: B 168 VAL cc_start: 0.8262 (t) cc_final: 0.7972 (p) REVERT: B 171 ASP cc_start: 0.7096 (t0) cc_final: 0.6533 (t0) REVERT: B 172 PHE cc_start: 0.8066 (m-10) cc_final: 0.7498 (m-10) REVERT: B 178 MET cc_start: 0.7692 (mmt) cc_final: 0.7351 (mmm) REVERT: B 210 LEU cc_start: 0.8418 (mm) cc_final: 0.7878 (tp) REVERT: B 252 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6920 (ttp80) REVERT: B 260 CYS cc_start: 0.6018 (OUTLIER) cc_final: 0.4648 (m) REVERT: B 261 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7145 (mmtt) REVERT: B 263 THR cc_start: 0.8482 (m) cc_final: 0.8157 (p) REVERT: B 271 ASN cc_start: 0.7944 (t0) cc_final: 0.7319 (m-40) REVERT: B 286 SER cc_start: 0.7097 (m) cc_final: 0.6822 (m) REVERT: B 309 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7513 (mtt180) REVERT: B 364 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 369 LEU cc_start: 0.8338 (mt) cc_final: 0.8022 (mt) REVERT: B 374 VAL cc_start: 0.8230 (m) cc_final: 0.7891 (t) REVERT: B 382 THR cc_start: 0.2909 (OUTLIER) cc_final: 0.2468 (m) REVERT: B 396 LYS cc_start: 0.7760 (mttt) cc_final: 0.7327 (mttm) REVERT: B 399 LYS cc_start: 0.7059 (mtpp) cc_final: 0.6645 (mtpp) REVERT: B 415 THR cc_start: 0.7670 (p) cc_final: 0.7209 (t) REVERT: B 454 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7659 (mmtt) REVERT: B 458 ASP cc_start: 0.7858 (t0) cc_final: 0.7433 (t0) REVERT: B 487 LYS cc_start: 0.7807 (pttp) cc_final: 0.7385 (pttp) REVERT: B 502 THR cc_start: 0.8227 (p) cc_final: 0.7948 (t) REVERT: B 533 ARG cc_start: 0.6791 (tpp-160) cc_final: 0.6567 (tpp-160) REVERT: B 618 HIS cc_start: 0.6957 (m-70) cc_final: 0.6594 (m90) outliers start: 33 outliers final: 22 residues processed: 309 average time/residue: 0.1349 time to fit residues: 55.0412 Evaluate side-chains 315 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 66 GLU 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 260 CYS Chi-restraints excluded: chain A residue 274 THR 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 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 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 274 THR 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 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: 0.6980 chunk 94 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 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 493 ASN ** 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 = 0.4027 r_free = 0.4027 target = 0.157440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132890 restraints weight = 15204.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137287 restraints weight = 7697.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140207 restraints weight = 4701.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142233 restraints weight = 3272.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143593 restraints weight = 2486.021| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10340 Z= 0.169 Angle : 0.726 9.772 14036 Z= 0.361 Chirality : 0.050 0.352 1550 Planarity : 0.004 0.060 1814 Dihedral : 5.991 42.312 1376 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.12 % Allowed : 16.34 % Favored : 80.54 % 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: -1.74 (0.23), residues: 1272 helix: -1.03 (0.85), residues: 38 sheet: -1.93 (0.69), residues: 54 loop : -1.25 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 53 TYR 0.019 0.002 TYR C 37 PHE 0.021 0.002 PHE B 404 TRP 0.051 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10276) covalent geometry : angle 0.69990 / 0.35 (13896) SS BOND : bond 0.00445 / 0.30 ( 52) SS BOND : angle 1.50868 / 0.96 ( 104) hydrogen bonds : bond 0.03726 / 2.42 ( 138) hydrogen bonds : angle 6.36916 / 4.28 ( 252) link_ALPHA1-3 : bond 0.00763 / 0.38 ( 2) link_ALPHA1-3 : angle 1.51805 / 0.76 ( 6) link_BETA1-3 : bond 0.00616 / 0.30 ( 2) link_BETA1-3 : angle 2.88326 / 1.56 ( 6) link_BETA1-4 : bond 0.00762 / 0.38 ( 2) link_BETA1-4 : angle 1.76403 / 0.90 ( 6) link_NAG-ASN : bond 0.00588 / 0.30 ( 6) link_NAG-ASN : angle 3.91810 / 1.94 ( 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 332 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.421 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: 0.8035 (mm110) cc_final: 0.7560 (mt0) REVERT: A 37 LYS cc_start: 0.8002 (mttt) cc_final: 0.7772 (mttp) REVERT: A 58 CYS cc_start: 0.5259 (t) cc_final: 0.4965 (t) REVERT: A 59 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7137 (mt-10) REVERT: A 64 ASN cc_start: 0.8294 (m-40) cc_final: 0.7808 (m110) REVERT: A 66 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6189 (mt-10) REVERT: A 73 ASN cc_start: 0.7751 (m-40) cc_final: 0.7295 (m-40) REVERT: A 80 LYS cc_start: 0.8329 (mttt) cc_final: 0.7652 (mttt) REVERT: A 83 GLN cc_start: 0.7279 (mt0) cc_final: 0.6779 (mt0) REVERT: A 125 TYR cc_start: 0.7944 (p90) cc_final: 0.7633 (p90) REVERT: A 171 ASP cc_start: 0.6650 (t0) cc_final: 0.6176 (t0) REVERT: A 172 PHE cc_start: 0.7878 (m-10) cc_final: 0.7245 (m-10) REVERT: A 210 LEU cc_start: 0.8442 (mm) cc_final: 0.8140 (mm) REVERT: A 335 LYS cc_start: 0.7501 (tptp) cc_final: 0.7295 (tptp) REVERT: A 340 ILE cc_start: 0.8297 (mp) cc_final: 0.7941 (mt) REVERT: A 357 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 361 ASN cc_start: 0.7091 (t0) cc_final: 0.6669 (t0) REVERT: A 382 THR cc_start: 0.2171 (OUTLIER) cc_final: 0.1917 (m) REVERT: A 399 LYS cc_start: 0.7154 (mtpp) cc_final: 0.6786 (mtpp) REVERT: A 405 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7231 (tp) REVERT: A 452 SER cc_start: 0.7404 (p) cc_final: 0.6781 (t) REVERT: A 454 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7604 (mmtt) REVERT: A 458 ASP cc_start: 0.7839 (t0) cc_final: 0.7384 (t0) REVERT: A 460 ASP cc_start: 0.6480 (m-30) cc_final: 0.6028 (m-30) REVERT: A 489 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7596 (mtmt) REVERT: A 521 ARG cc_start: 0.7433 (ppt-90) cc_final: 0.6948 (ppt-90) REVERT: A 618 HIS cc_start: 0.7073 (m-70) cc_final: 0.6688 (m-70) REVERT: D 15 LEU cc_start: 0.8259 (mm) cc_final: 0.7974 (mt) REVERT: B 54 MET cc_start: 0.8040 (tpp) cc_final: 0.7434 (tpp) REVERT: B 59 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 66 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6250 (mt-10) REVERT: B 80 LYS cc_start: 0.8439 (mttt) cc_final: 0.7804 (mttt) REVERT: B 98 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7272 (mmm-85) REVERT: B 139 ASN cc_start: 0.7850 (m110) cc_final: 0.7602 (m-40) REVERT: B 168 VAL cc_start: 0.8309 (t) cc_final: 0.7952 (p) REVERT: B 171 ASP cc_start: 0.7123 (t0) cc_final: 0.6549 (t0) REVERT: B 172 PHE cc_start: 0.7968 (m-10) cc_final: 0.7404 (m-10) REVERT: B 210 LEU cc_start: 0.8390 (mm) cc_final: 0.7822 (tp) REVERT: B 252 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6836 (ttp80) REVERT: B 260 CYS cc_start: 0.6027 (OUTLIER) cc_final: 0.4299 (m) REVERT: B 261 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7137 (mmtt) REVERT: B 263 THR cc_start: 0.8528 (m) cc_final: 0.8213 (p) REVERT: B 278 ASP cc_start: 0.7361 (m-30) cc_final: 0.6879 (m-30) REVERT: B 286 SER cc_start: 0.7147 (m) cc_final: 0.6865 (m) REVERT: B 309 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7520 (mtt180) REVERT: B 350 SER cc_start: 0.7180 (t) cc_final: 0.6937 (p) REVERT: B 364 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 374 VAL cc_start: 0.8192 (m) cc_final: 0.7989 (t) REVERT: B 382 THR cc_start: 0.3223 (OUTLIER) cc_final: 0.2933 (m) REVERT: B 396 LYS cc_start: 0.7777 (mttt) cc_final: 0.7333 (mttm) REVERT: B 399 LYS cc_start: 0.7108 (mtpp) cc_final: 0.6633 (mtpp) REVERT: B 404 PHE cc_start: 0.8025 (p90) cc_final: 0.7429 (p90) REVERT: B 415 THR cc_start: 0.7646 (p) cc_final: 0.7127 (t) REVERT: B 454 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7650 (mmtt) REVERT: B 458 ASP cc_start: 0.7853 (t0) cc_final: 0.7388 (t0) REVERT: B 487 LYS cc_start: 0.7847 (pttp) cc_final: 0.7432 (pttp) REVERT: B 502 THR cc_start: 0.8235 (p) cc_final: 0.7963 (t) REVERT: B 618 HIS cc_start: 0.6920 (m-70) cc_final: 0.6559 (m90) outliers start: 35 outliers final: 19 residues processed: 313 average time/residue: 0.1308 time to fit residues: 54.2880 Evaluate side-chains 318 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 66 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 LEU 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 263 THR 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 C residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 83 GLN 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 252 ARG Chi-restraints excluded: chain B residue 260 CYS 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: 0.3980 chunk 117 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 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 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132218 restraints weight = 15139.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136603 restraints weight = 7718.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139562 restraints weight = 4746.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141611 restraints weight = 3298.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142937 restraints weight = 2516.556| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.6311 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= 0.203 Angle : 0.770 9.740 14036 Z= 0.383 Chirality : 0.051 0.347 1550 Planarity : 0.004 0.055 1814 Dihedral : 6.189 43.511 1376 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.48 % Allowed : 17.23 % Favored : 79.29 % 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 (0.23), residues: 1272 helix: -1.20 (0.83), residues: 38 sheet: -2.02 (0.68), residues: 54 loop : -1.21 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 414 TYR 0.020 0.002 TYR D 37 PHE 0.018 0.002 PHE A 78 TRP 0.059 0.002 TRP C 49 HIS 0.009 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (10276) covalent geometry : angle 0.74214 / 0.38 (13896) SS BOND : bond 0.00456 / 0.30 ( 52) SS BOND : angle 1.62317 / 1.06 ( 104) hydrogen bonds : bond 0.03967 / 2.57 ( 138) hydrogen bonds : angle 6.43547 / 4.28 ( 252) link_ALPHA1-3 : bond 0.00816 / 0.41 ( 2) link_ALPHA1-3 : angle 1.59323 / 0.79 ( 6) link_BETA1-3 : bond 0.00345 / 0.17 ( 2) link_BETA1-3 : angle 2.86356 / 1.54 ( 6) link_BETA1-4 : bond 0.00638 / 0.32 ( 2) link_BETA1-4 : angle 1.76770 / 0.90 ( 6) link_NAG-ASN : bond 0.00775 / 0.39 ( 6) link_NAG-ASN : angle 4.13487 / 2.03 ( 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 346 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 0.412 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: 0.8044 (mm110) cc_final: 0.7581 (mt0) REVERT: A 58 CYS cc_start: 0.5310 (t) cc_final: 0.4995 (t) REVERT: A 59 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 64 ASN cc_start: 0.8230 (m-40) cc_final: 0.7482 (m110) REVERT: A 73 ASN cc_start: 0.7626 (m110) cc_final: 0.7353 (m-40) REVERT: A 80 LYS cc_start: 0.8359 (mttt) cc_final: 0.7695 (mttt) REVERT: A 83 GLN cc_start: 0.7321 (mt0) cc_final: 0.6848 (mt0) REVERT: A 125 TYR cc_start: 0.7957 (p90) cc_final: 0.7739 (p90) REVERT: A 171 ASP cc_start: 0.6755 (t0) cc_final: 0.6210 (t0) REVERT: A 172 PHE cc_start: 0.7865 (m-10) cc_final: 0.7235 (m-10) REVERT: A 198 SER cc_start: 0.6498 (m) cc_final: 0.6283 (t) REVERT: A 210 LEU cc_start: 0.8431 (mm) cc_final: 0.8158 (mm) REVERT: A 253 LYS cc_start: 0.8312 (mttp) cc_final: 0.8058 (mttp) REVERT: A 335 LYS cc_start: 0.7507 (tptp) cc_final: 0.7298 (tptp) REVERT: A 340 ILE cc_start: 0.8361 (mp) cc_final: 0.8016 (mt) REVERT: A 357 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7804 (mtmm) REVERT: A 361 ASN cc_start: 0.7092 (t0) cc_final: 0.6659 (t0) REVERT: A 382 THR cc_start: 0.2357 (OUTLIER) cc_final: 0.2104 (m) REVERT: A 399 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6829 (mtpp) REVERT: A 405 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 452 SER cc_start: 0.7456 (p) cc_final: 0.6871 (t) REVERT: A 454 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7659 (mmtt) REVERT: A 458 ASP cc_start: 0.7841 (t0) cc_final: 0.7349 (t0) REVERT: A 460 ASP cc_start: 0.6480 (m-30) cc_final: 0.6254 (m-30) REVERT: A 521 ARG cc_start: 0.7382 (ppt-90) cc_final: 0.6942 (ppt-90) REVERT: A 531 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6626 (ttm170) REVERT: A 586 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6768 (tp) REVERT: A 618 HIS cc_start: 0.7092 (m-70) cc_final: 0.6699 (m-70) REVERT: D 37 TYR cc_start: 0.8306 (m-80) cc_final: 0.8089 (m-10) REVERT: B 54 MET cc_start: 0.7979 (tpp) cc_final: 0.7280 (tpp) REVERT: B 59 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7247 (mt-10) REVERT: B 66 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6197 (mt-10) REVERT: B 80 LYS cc_start: 0.8466 (mttt) cc_final: 0.7830 (mttt) REVERT: B 98 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7428 (mmm-85) REVERT: B 138 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7864 (mtm-85) REVERT: B 139 ASN cc_start: 0.7879 (m110) cc_final: 0.7558 (m-40) REVERT: B 168 VAL cc_start: 0.8362 (t) cc_final: 0.7972 (p) REVERT: B 171 ASP cc_start: 0.7210 (t0) cc_final: 0.6681 (t0) REVERT: B 172 PHE cc_start: 0.7945 (m-10) cc_final: 0.7375 (m-10) REVERT: B 210 LEU cc_start: 0.8373 (mm) cc_final: 0.7850 (tp) REVERT: B 252 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6836 (ttp80) REVERT: B 260 CYS cc_start: 0.6220 (OUTLIER) cc_final: 0.4487 (m) REVERT: B 261 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7179 (mmtt) REVERT: B 263 THR cc_start: 0.8525 (m) cc_final: 0.8237 (p) REVERT: B 278 ASP cc_start: 0.7361 (m-30) cc_final: 0.6905 (m-30) REVERT: B 286 SER cc_start: 0.7181 (m) cc_final: 0.6903 (m) REVERT: B 293 LYS cc_start: 0.8373 (mttm) cc_final: 0.8121 (mttm) REVERT: B 309 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7574 (mtt180) REVERT: B 340 ILE cc_start: 0.8215 (mm) cc_final: 0.7958 (mm) REVERT: B 350 SER cc_start: 0.7149 (t) cc_final: 0.6930 (p) REVERT: B 364 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 382 THR cc_start: 0.3507 (OUTLIER) cc_final: 0.3218 (m) REVERT: B 396 LYS cc_start: 0.7778 (mttt) cc_final: 0.6733 (mtpp) REVERT: B 399 LYS cc_start: 0.7153 (mtpp) cc_final: 0.6688 (mtpp) REVERT: B 404 PHE cc_start: 0.8063 (p90) cc_final: 0.7600 (p90) REVERT: B 415 THR cc_start: 0.7705 (p) cc_final: 0.7191 (t) REVERT: B 454 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7650 (mmtt) REVERT: B 458 ASP cc_start: 0.7889 (t0) cc_final: 0.7460 (t0) REVERT: B 487 LYS cc_start: 0.7918 (pttp) cc_final: 0.7524 (pttp) REVERT: B 502 THR cc_start: 0.8341 (p) cc_final: 0.8057 (t) REVERT: B 561 GLU cc_start: 0.6755 (tp30) cc_final: 0.5658 (tm-30) REVERT: B 618 HIS cc_start: 0.6963 (m-70) cc_final: 0.6596 (m90) outliers start: 39 outliers final: 21 residues processed: 324 average time/residue: 0.1321 time to fit residues: 56.3343 Evaluate side-chains 325 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 269 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 400 GLU 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 37 TYR Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN 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 111 MET Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 105 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.158304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133378 restraints weight = 15075.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137811 restraints weight = 7741.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140790 restraints weight = 4773.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142858 restraints weight = 3332.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144247 restraints weight = 2540.879| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10340 Z= 0.146 Angle : 0.738 10.267 14036 Z= 0.365 Chirality : 0.050 0.344 1550 Planarity : 0.004 0.060 1814 Dihedral : 5.960 39.401 1376 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.86 % Allowed : 17.41 % Favored : 79.73 % 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: -1.58 (0.24), residues: 1272 helix: -1.17 (0.84), residues: 38 sheet: -1.87 (0.68), residues: 54 loop : -1.12 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 527 TYR 0.016 0.002 TYR D 37 PHE 0.017 0.002 PHE B 404 TRP 0.049 0.002 TRP C 49 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10276) covalent geometry : angle 0.71600 / 0.36 (13896) SS BOND : bond 0.00392 / 0.25 ( 52) SS BOND : angle 1.32227 / 0.87 ( 104) hydrogen bonds : bond 0.03716 / 2.41 ( 138) hydrogen bonds : angle 6.39410 / 4.27 ( 252) link_ALPHA1-3 : bond 0.00814 / 0.41 ( 2) link_ALPHA1-3 : angle 1.53281 / 0.77 ( 6) link_BETA1-3 : bond 0.00564 / 0.28 ( 2) link_BETA1-3 : angle 2.90175 / 1.58 ( 6) link_BETA1-4 : bond 0.00683 / 0.34 ( 2) link_BETA1-4 : angle 1.74839 / 0.87 ( 6) link_NAG-ASN : bond 0.00528 / 0.30 ( 6) link_NAG-ASN : angle 3.76974 / 1.88 ( 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: 32 poor density : 294 time to evaluate : 0.390 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: 0.7998 (mm110) cc_final: 0.7593 (mt0) REVERT: A 58 CYS cc_start: 0.5301 (t) cc_final: 0.5003 (t) REVERT: A 59 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 66 GLU cc_start: 0.6628 (mp0) cc_final: 0.6119 (mp0) REVERT: A 80 LYS cc_start: 0.8374 (mttt) cc_final: 0.7848 (mttt) REVERT: A 83 GLN cc_start: 0.7302 (mt0) cc_final: 0.6837 (mt0) REVERT: A 125 TYR cc_start: 0.7967 (p90) cc_final: 0.7726 (p90) REVERT: A 171 ASP cc_start: 0.6670 (t0) cc_final: 0.6204 (t0) REVERT: A 172 PHE cc_start: 0.7832 (m-10) cc_final: 0.7245 (m-10) REVERT: A 210 LEU cc_start: 0.8429 (mm) cc_final: 0.8153 (mm) REVERT: A 253 LYS cc_start: 0.8334 (mttp) cc_final: 0.8102 (mttp) REVERT: A 340 ILE cc_start: 0.8274 (mp) cc_final: 0.7919 (mt) REVERT: A 357 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7789 (mtmm) REVERT: A 361 ASN cc_start: 0.7100 (t0) cc_final: 0.6635 (t0) REVERT: A 382 THR cc_start: 0.2312 (OUTLIER) cc_final: 0.2079 (m) REVERT: A 399 LYS cc_start: 0.7139 (mtpp) cc_final: 0.6760 (mtpp) REVERT: A 405 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7295 (tp) REVERT: A 452 SER cc_start: 0.7432 (p) cc_final: 0.6619 (t) REVERT: A 454 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7571 (mmtt) REVERT: A 458 ASP cc_start: 0.7766 (t0) cc_final: 0.7179 (t0) REVERT: A 460 ASP cc_start: 0.6474 (m-30) cc_final: 0.6163 (m-30) REVERT: A 489 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7699 (mtmt) REVERT: A 521 ARG cc_start: 0.7410 (ppt-90) cc_final: 0.6860 (ppt-90) REVERT: A 522 ASP cc_start: 0.6821 (t0) cc_final: 0.6409 (t0) REVERT: A 600 MET cc_start: 0.6271 (tpp) cc_final: 0.5700 (tpp) REVERT: A 618 HIS cc_start: 0.7182 (m-70) cc_final: 0.6896 (m-70) REVERT: B 54 MET cc_start: 0.7895 (tpp) cc_final: 0.7394 (tpp) REVERT: B 59 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 66 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6112 (mt-10) REVERT: B 80 LYS cc_start: 0.8436 (mttt) cc_final: 0.7818 (mttt) REVERT: B 98 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7416 (mmm-85) REVERT: B 138 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7851 (mtm-85) REVERT: B 139 ASN cc_start: 0.7838 (m110) cc_final: 0.7502 (m-40) REVERT: B 168 VAL cc_start: 0.8272 (t) cc_final: 0.7888 (p) REVERT: B 171 ASP cc_start: 0.7196 (t0) cc_final: 0.6667 (t0) REVERT: B 172 PHE cc_start: 0.7807 (m-10) cc_final: 0.7301 (m-10) REVERT: B 210 LEU cc_start: 0.8372 (mm) cc_final: 0.7842 (tp) REVERT: B 252 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6826 (ttp80) REVERT: B 260 CYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5128 (m) REVERT: B 263 THR cc_start: 0.8453 (m) cc_final: 0.8176 (p) REVERT: B 277 MET cc_start: 0.7203 (mmm) cc_final: 0.6880 (mmm) REVERT: B 278 ASP cc_start: 0.7345 (m-30) cc_final: 0.6914 (m-30) REVERT: B 286 SER cc_start: 0.7139 (m) cc_final: 0.6875 (m) REVERT: B 293 LYS cc_start: 0.8366 (mttm) cc_final: 0.8100 (mttm) REVERT: B 364 SER cc_start: 0.8829 (p) cc_final: 0.8502 (m) REVERT: B 382 THR cc_start: 0.3479 (OUTLIER) cc_final: 0.3222 (m) REVERT: B 399 LYS cc_start: 0.7089 (mtpp) cc_final: 0.6655 (mtpp) REVERT: B 404 PHE cc_start: 0.8120 (p90) cc_final: 0.7766 (p90) REVERT: B 454 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7671 (mmtt) REVERT: B 458 ASP cc_start: 0.7841 (t0) cc_final: 0.7343 (t0) REVERT: B 487 LYS cc_start: 0.7844 (pttp) cc_final: 0.7465 (pttp) REVERT: B 502 THR cc_start: 0.8347 (p) cc_final: 0.8098 (t) REVERT: B 521 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7228 (ptt-90) REVERT: B 561 GLU cc_start: 0.6405 (tp30) cc_final: 0.4466 (tm-30) REVERT: B 618 HIS cc_start: 0.7004 (m-70) cc_final: 0.6622 (m90) outliers start: 32 outliers final: 20 residues processed: 308 average time/residue: 0.1351 time to fit residues: 54.7244 Evaluate side-chains 315 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR 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 351 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 400 GLU 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 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 32 GLN 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 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 562 CYS 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: 1.9990 chunk 19 optimal weight: 0.2980 chunk 121 optimal weight: 0.0270 chunk 26 optimal weight: 0.0770 chunk 41 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 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 408 GLN ** 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 = 0.4029 r_free = 0.4029 target = 0.158954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134387 restraints weight = 15120.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138824 restraints weight = 7706.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141826 restraints weight = 4724.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143911 restraints weight = 3273.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145175 restraints weight = 2480.058| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10340 Z= 0.135 Angle : 0.757 10.443 14036 Z= 0.376 Chirality : 0.050 0.342 1550 Planarity : 0.004 0.059 1814 Dihedral : 5.962 38.093 1376 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.41 % Allowed : 18.75 % Favored : 78.84 % 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: -1.61 (0.24), residues: 1272 helix: -1.96 (0.69), residues: 50 sheet: -1.81 (0.68), residues: 54 loop : -1.11 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 149 TYR 0.026 0.002 TYR D 37 PHE 0.025 0.002 PHE A 404 TRP 0.042 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10276) covalent geometry : angle 0.73694 / 0.37 (13896) SS BOND : bond 0.00391 / 0.26 ( 52) SS BOND : angle 1.30423 / 0.87 ( 104) hydrogen bonds : bond 0.03665 / 2.35 ( 138) hydrogen bonds : angle 6.44551 / 4.24 ( 252) link_ALPHA1-3 : bond 0.00793 / 0.40 ( 2) link_ALPHA1-3 : angle 1.52045 / 0.77 ( 6) link_BETA1-3 : bond 0.00681 / 0.34 ( 2) link_BETA1-3 : angle 2.93897 / 1.60 ( 6) link_BETA1-4 : bond 0.00821 / 0.41 ( 2) link_BETA1-4 : angle 1.71330 / 0.85 ( 6) link_NAG-ASN : bond 0.00491 / 0.29 ( 6) link_NAG-ASN : angle 3.62588 / 1.81 ( 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 318 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.399 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: 0.7969 (mm110) cc_final: 0.7631 (mt0) REVERT: A 54 MET cc_start: 0.7785 (tpp) cc_final: 0.6905 (tpp) REVERT: A 58 CYS cc_start: 0.5285 (t) cc_final: 0.5060 (t) REVERT: A 59 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 80 LYS cc_start: 0.8306 (mttt) cc_final: 0.7736 (mttt) REVERT: A 83 GLN cc_start: 0.7341 (mt0) cc_final: 0.6830 (mt0) REVERT: A 111 MET cc_start: 0.7159 (ptm) cc_final: 0.6904 (ppp) REVERT: A 171 ASP cc_start: 0.6659 (t0) cc_final: 0.6246 (t0) REVERT: A 172 PHE cc_start: 0.7819 (m-10) cc_final: 0.7247 (m-10) REVERT: A 210 LEU cc_start: 0.8413 (mm) cc_final: 0.8130 (mm) REVERT: A 253 LYS cc_start: 0.8287 (mttp) cc_final: 0.7975 (mttp) REVERT: A 357 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7765 (mtmm) REVERT: A 361 ASN cc_start: 0.7075 (t0) cc_final: 0.6660 (t0) REVERT: A 382 THR cc_start: 0.2354 (OUTLIER) cc_final: 0.2108 (m) REVERT: A 399 LYS cc_start: 0.7101 (mtpp) cc_final: 0.6733 (mtpp) REVERT: A 405 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7263 (tp) REVERT: A 452 SER cc_start: 0.7390 (p) cc_final: 0.6603 (t) REVERT: A 454 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7568 (mmtt) REVERT: A 458 ASP cc_start: 0.7706 (t0) cc_final: 0.7142 (t0) REVERT: A 521 ARG cc_start: 0.7395 (ppt-90) cc_final: 0.6829 (ppt-90) REVERT: A 522 ASP cc_start: 0.6886 (t0) cc_final: 0.6430 (t0) REVERT: A 600 MET cc_start: 0.6294 (tpp) cc_final: 0.5698 (tpp) REVERT: A 618 HIS cc_start: 0.7159 (m-70) cc_final: 0.6861 (m-70) REVERT: B 54 MET cc_start: 0.7823 (tpp) cc_final: 0.7433 (tpp) REVERT: B 66 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6097 (mt-10) REVERT: B 80 LYS cc_start: 0.8435 (mttt) cc_final: 0.7830 (mttt) REVERT: B 83 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: B 98 ARG cc_start: 0.7714 (ttt90) cc_final: 0.7357 (mmm-85) REVERT: B 139 ASN cc_start: 0.7811 (m110) cc_final: 0.7430 (m-40) REVERT: B 168 VAL cc_start: 0.8254 (t) cc_final: 0.7873 (p) REVERT: B 171 ASP cc_start: 0.7238 (t0) cc_final: 0.6813 (t0) REVERT: B 172 PHE cc_start: 0.7773 (m-10) cc_final: 0.7261 (m-10) REVERT: B 210 LEU cc_start: 0.8361 (mm) cc_final: 0.7819 (tp) REVERT: B 252 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6808 (ttp80) REVERT: B 260 CYS cc_start: 0.6099 (OUTLIER) cc_final: 0.4083 (m) REVERT: B 261 LYS cc_start: 0.7565 (mmtt) cc_final: 0.7054 (mmtt) REVERT: B 263 THR cc_start: 0.8443 (m) cc_final: 0.8198 (p) REVERT: B 277 MET cc_start: 0.7202 (mmm) cc_final: 0.6729 (mmm) REVERT: B 278 ASP cc_start: 0.7315 (m-30) cc_final: 0.6891 (m-30) REVERT: B 286 SER cc_start: 0.7087 (m) cc_final: 0.6779 (m) REVERT: B 293 LYS cc_start: 0.8350 (mttm) cc_final: 0.8092 (mttm) REVERT: B 364 SER cc_start: 0.8820 (p) cc_final: 0.8499 (m) REVERT: B 382 THR cc_start: 0.3510 (OUTLIER) cc_final: 0.3215 (m) REVERT: B 399 LYS cc_start: 0.7046 (mtpp) cc_final: 0.6614 (mtpp) REVERT: B 404 PHE cc_start: 0.8129 (p90) cc_final: 0.7814 (p90) REVERT: B 414 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.6188 (mmm-85) REVERT: B 454 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7673 (mmtt) REVERT: B 458 ASP cc_start: 0.7760 (t0) cc_final: 0.7223 (t0) REVERT: B 521 ARG cc_start: 0.7445 (ptt-90) cc_final: 0.7131 (ptt-90) REVERT: B 561 GLU cc_start: 0.6376 (tp30) cc_final: 0.4734 (tm-30) REVERT: B 618 HIS cc_start: 0.6975 (m-70) cc_final: 0.6591 (m90) outliers start: 27 outliers final: 18 residues processed: 303 average time/residue: 0.1363 time to fit residues: 54.1429 Evaluate side-chains 313 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 39 THR 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 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 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 562 CYS 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: 0.9990 chunk 125 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 0.0060 chunk 38 optimal weight: 0.0770 chunk 80 optimal weight: 0.7980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 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 52 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.155460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131022 restraints weight = 14955.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135357 restraints weight = 7674.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138258 restraints weight = 4728.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140323 restraints weight = 3301.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141783 restraints weight = 2510.575| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.6917 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= 0.199 Angle : 0.801 9.735 14036 Z= 0.400 Chirality : 0.052 0.331 1550 Planarity : 0.004 0.056 1814 Dihedral : 6.164 41.280 1376 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.23 % Allowed : 19.38 % Favored : 78.39 % 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: -1.67 (0.23), residues: 1272 helix: -1.98 (0.69), residues: 50 sheet: -1.21 (0.90), residues: 34 loop : -1.19 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 53 TYR 0.020 0.002 TYR D 22 PHE 0.026 0.002 PHE A 404 TRP 0.047 0.002 TRP C 49 HIS 0.006 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (10276) covalent geometry : angle 0.77763 / 0.39 (13896) SS BOND : bond 0.00449 / 0.28 ( 52) SS BOND : angle 1.47744 / 0.98 ( 104) hydrogen bonds : bond 0.04088 / 2.65 ( 138) hydrogen bonds : angle 6.26989 / 4.16 ( 252) link_ALPHA1-3 : bond 0.00728 / 0.37 ( 2) link_ALPHA1-3 : angle 1.56932 / 0.78 ( 6) link_BETA1-3 : bond 0.00403 / 0.20 ( 2) link_BETA1-3 : angle 2.87564 / 1.55 ( 6) link_BETA1-4 : bond 0.00752 / 0.37 ( 2) link_BETA1-4 : angle 1.77850 / 0.89 ( 6) link_NAG-ASN : bond 0.00731 / 0.38 ( 6) link_NAG-ASN : angle 3.95936 / 1.96 ( 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 328 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.410 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: 0.7997 (mm110) cc_final: 0.7623 (mt0) REVERT: A 54 MET cc_start: 0.7822 (tpp) cc_final: 0.7079 (tpp) REVERT: A 58 CYS cc_start: 0.5300 (t) cc_final: 0.5054 (t) REVERT: A 59 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7160 (mt-10) REVERT: A 80 LYS cc_start: 0.8317 (mttt) cc_final: 0.7756 (mttt) REVERT: A 83 GLN cc_start: 0.7360 (mt0) cc_final: 0.6851 (mt0) REVERT: A 111 MET cc_start: 0.7294 (ptm) cc_final: 0.7035 (ppp) REVERT: A 152 ASN cc_start: 0.7520 (t0) cc_final: 0.7158 (t0) REVERT: A 171 ASP cc_start: 0.6767 (t0) cc_final: 0.6332 (t0) REVERT: A 172 PHE cc_start: 0.7841 (m-10) cc_final: 0.7244 (m-10) REVERT: A 210 LEU cc_start: 0.8432 (mm) cc_final: 0.8131 (mm) REVERT: A 253 LYS cc_start: 0.8228 (mttp) cc_final: 0.7871 (mttp) REVERT: A 357 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7820 (mtmm) REVERT: A 382 THR cc_start: 0.2819 (OUTLIER) cc_final: 0.2530 (m) REVERT: A 396 LYS cc_start: 0.7832 (mttt) cc_final: 0.7168 (mttm) REVERT: A 399 LYS cc_start: 0.7219 (mtpp) cc_final: 0.6825 (mtpp) REVERT: A 405 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7215 (tp) REVERT: A 452 SER cc_start: 0.7445 (p) cc_final: 0.6647 (t) REVERT: A 454 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7523 (mmtt) REVERT: A 458 ASP cc_start: 0.7776 (t0) cc_final: 0.7298 (t0) REVERT: A 521 ARG cc_start: 0.7444 (ppt-90) cc_final: 0.6874 (ppt-90) REVERT: A 522 ASP cc_start: 0.6837 (t0) cc_final: 0.6468 (t0) REVERT: A 600 MET cc_start: 0.6343 (tpp) cc_final: 0.5751 (tpp) REVERT: A 618 HIS cc_start: 0.7036 (m-70) cc_final: 0.6635 (m170) REVERT: C 21 MET cc_start: 0.7537 (ptt) cc_final: 0.7334 (ptt) REVERT: B 54 MET cc_start: 0.7711 (tpp) cc_final: 0.7148 (tpp) REVERT: B 66 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6105 (mt-10) REVERT: B 80 LYS cc_start: 0.8483 (mttt) cc_final: 0.7844 (mttt) REVERT: B 98 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7521 (mmm-85) REVERT: B 139 ASN cc_start: 0.7956 (m110) cc_final: 0.7702 (m-40) REVERT: B 168 VAL cc_start: 0.8266 (t) cc_final: 0.7887 (p) REVERT: B 171 ASP cc_start: 0.7283 (t0) cc_final: 0.7039 (t0) REVERT: B 210 LEU cc_start: 0.8301 (mm) cc_final: 0.7831 (tp) REVERT: B 260 CYS cc_start: 0.6413 (OUTLIER) cc_final: 0.4545 (m) REVERT: B 261 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7133 (mmtt) REVERT: B 263 THR cc_start: 0.8467 (m) cc_final: 0.8186 (p) REVERT: B 278 ASP cc_start: 0.7278 (m-30) cc_final: 0.6865 (m-30) REVERT: B 286 SER cc_start: 0.7211 (m) cc_final: 0.6888 (m) REVERT: B 293 LYS cc_start: 0.8347 (mttm) cc_final: 0.8066 (mttm) REVERT: B 364 SER cc_start: 0.8837 (p) cc_final: 0.8495 (m) REVERT: B 382 THR cc_start: 0.3851 (OUTLIER) cc_final: 0.3560 (m) REVERT: B 399 LYS cc_start: 0.7039 (mtpp) cc_final: 0.6605 (mtpp) REVERT: B 404 PHE cc_start: 0.8104 (p90) cc_final: 0.7806 (p90) REVERT: B 454 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7671 (mmtt) REVERT: B 458 ASP cc_start: 0.7891 (t0) cc_final: 0.7337 (t0) REVERT: B 561 GLU cc_start: 0.6410 (tp30) cc_final: 0.4877 (tm-30) REVERT: B 618 HIS cc_start: 0.7146 (m-70) cc_final: 0.6764 (m90) outliers start: 25 outliers final: 18 residues processed: 314 average time/residue: 0.1383 time to fit residues: 56.9073 Evaluate side-chains 317 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 256 ASP 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 C residue 50 TRP Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN 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 111 MET Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 562 CYS 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: 0.7980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 0.0270 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 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 408 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.156665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132195 restraints weight = 15127.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136627 restraints weight = 7715.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139558 restraints weight = 4727.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141616 restraints weight = 3287.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143025 restraints weight = 2497.157| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10340 Z= 0.158 Angle : 0.785 9.796 14036 Z= 0.390 Chirality : 0.051 0.347 1550 Planarity : 0.005 0.092 1814 Dihedral : 6.120 38.381 1376 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.05 % Allowed : 20.71 % Favored : 77.23 % 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: -1.62 (0.23), residues: 1272 helix: -2.00 (0.69), residues: 50 sheet: -1.11 (0.91), residues: 34 loop : -1.16 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 527 TYR 0.023 0.002 TYR D 22 PHE 0.025 0.002 PHE A 404 TRP 0.061 0.003 TRP D 49 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10276) covalent geometry : angle 0.76178 / 0.38 (13896) SS BOND : bond 0.00383 / 0.24 ( 52) SS BOND : angle 1.49894 / 0.98 ( 104) hydrogen bonds : bond 0.03872 / 2.54 ( 138) hydrogen bonds : angle 6.25740 / 4.13 ( 252) link_ALPHA1-3 : bond 0.00749 / 0.38 ( 2) link_ALPHA1-3 : angle 1.52903 / 0.77 ( 6) link_BETA1-3 : bond 0.00591 / 0.29 ( 2) link_BETA1-3 : angle 2.91546 / 1.59 ( 6) link_BETA1-4 : bond 0.00809 / 0.40 ( 2) link_BETA1-4 : angle 1.85817 / 0.91 ( 6) link_NAG-ASN : bond 0.00539 / 0.30 ( 6) link_NAG-ASN : angle 3.76790 / 1.88 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.06 seconds wall clock time: 37 minutes 45.87 seconds (2265.87 seconds total)