Starting phenix.real_space_refine on Mon Jun 16 05:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_34746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_34746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_34746.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_34746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgs_34746/06_2025/8hgs_34746.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4577 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.88, per 1000 atoms: 0.58 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: 2.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.43 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: 3.02 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3386 1.35 - 1.47: 2225 1.47 - 1.59: 4515 1.59 - 1.71: 2 1.71 - 1.83: 148 Bond restraints: 10276 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.591 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.464 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13492 1.90 - 3.81: 326 3.81 - 5.71: 56 5.71 - 7.61: 14 7.61 - 9.52: 8 Bond angle restraints: 13896 Sorted by residual: angle pdb=" N ALA A 258 " pdb=" CA ALA A 258 " pdb=" C ALA A 258 " ideal model delta sigma weight residual 114.64 108.32 6.32 1.52e+00 4.33e-01 1.73e+01 angle pdb=" N ALA B 258 " pdb=" CA ALA B 258 " pdb=" C ALA B 258 " ideal model delta sigma weight residual 114.64 108.33 6.31 1.52e+00 4.33e-01 1.72e+01 angle pdb=" C CYS B 470 " pdb=" N TYR B 471 " pdb=" CA TYR B 471 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C CYS A 470 " pdb=" N TYR A 471 " pdb=" CA TYR A 471 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N TYR A 471 " pdb=" CA TYR A 471 " pdb=" C TYR A 471 " ideal model delta sigma weight residual 110.80 118.50 -7.70 2.13e+00 2.20e-01 1.31e+01 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 6264 21.18 - 42.35: 170 42.35 - 63.53: 48 63.53 - 84.71: 26 84.71 - 105.88: 28 Dihedral angle restraints: 6536 sinusoidal: 2860 harmonic: 3676 Sorted by residual: dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 20 " pdb=" CB CYS D 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C 6 " pdb=" SG CYS C 6 " pdb=" SG CYS C 20 " pdb=" CB CYS C 20 " ideal model delta sinusoidal sigma weight residual 93.00 150.02 -57.02 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -137.77 51.77 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 6533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1365 0.087 - 0.174: 175 0.174 - 0.261: 5 0.261 - 0.348: 3 0.348 - 0.436: 2 Chirality restraints: 1550 Sorted by residual: chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1547 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 256 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C ASP B 256 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 256 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ASP A 256 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 256 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 257 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 511 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO B 512 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.032 5.00e-02 4.00e+02 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3241 2.87 - 3.38: 8786 3.38 - 3.89: 16257 3.89 - 4.39: 17676 4.39 - 4.90: 30946 Nonbonded interactions: 76906 Sorted by model distance: nonbonded pdb=" OH TYR D 22 " pdb=" OD1 ASP D 27 " model vdw 2.368 3.040 nonbonded pdb=" OH TYR C 22 " pdb=" OD1 ASP C 27 " model vdw 2.368 3.040 nonbonded pdb=" OG1 THR A 302 " pdb=" OG SER A 306 " model vdw 2.379 3.040 nonbonded pdb=" O ARG B 309 " pdb=" NH1 ARG B 429 " model vdw 2.379 3.120 nonbonded pdb=" OG1 THR B 302 " pdb=" OG SER B 306 " model vdw 2.380 3.040 ... (remaining 76901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10340 Z= 0.205 Angle : 0.788 12.885 14036 Z= 0.405 Chirality : 0.057 0.436 1550 Planarity : 0.006 0.058 1814 Dihedral : 13.676 105.883 4020 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (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 TRP 0.005 0.001 TRP D 50 HIS 0.006 0.001 HIS A 47 PHE 0.021 0.002 PHE A 404 TYR 0.013 0.001 TYR A 88 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 6) link_NAG-ASN : angle 4.99238 ( 18) link_BETA1-4 : bond 0.01613 ( 2) link_BETA1-4 : angle 1.91480 ( 6) link_ALPHA1-3 : bond 0.01502 ( 2) link_ALPHA1-3 : angle 2.28169 ( 6) hydrogen bonds : bond 0.21724 ( 138) hydrogen bonds : angle 6.98730 ( 252) SS BOND : bond 0.00330 ( 52) SS BOND : angle 1.08813 ( 104) link_BETA1-3 : bond 0.01574 ( 2) link_BETA1-3 : angle 7.29947 ( 6) covalent geometry : bond 0.00394 (10276) covalent geometry : angle 0.74831 (13896) *********************** 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 : 1.263 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: 0.8191 (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: 0.6847 (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: 0.6535 (ttt90) cc_final: 0.6286 (ttt-90) REVERT: A 249 LEU cc_start: 0.7802 (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: 0.7178 (t0) cc_final: 0.6800 (t0) REVERT: A 462 ILE cc_start: 0.6221 (tt) cc_final: 0.5917 (tt) REVERT: A 541 LEU cc_start: 0.6522 (mt) cc_final: 0.6226 (mp) REVERT: A 618 HIS cc_start: 0.6176 (m-70) cc_final: 0.5735 (m90) REVERT: C 21 MET cc_start: 0.7008 (ptt) cc_final: 0.6602 (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: 0.7443 (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: 0.7510 (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: 0.5945 (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: 0.7578 (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: 0.2864 time to fit residues: 121.4621 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.0870 chunk 114 optimal weight: 0.0470 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 94 ASN A 139 ASN A 338 ASN A 432 GLN A 433 HIS A 468 ASN A 552 ASN A 559 HIS C 10 HIS D 10 HIS D 16 HIS B 47 HIS ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 432 GLN B 433 HIS B 468 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150834 restraints weight = 15475.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155582 restraints weight = 7731.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158762 restraints weight = 4700.664| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 10340 Z= 0.196 Angle : 0.766 13.198 14036 Z= 0.378 Chirality : 0.053 0.298 1550 Planarity : 0.005 0.064 1814 Dihedral : 13.066 83.989 1620 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.96 % Allowed : 8.48 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.21), residues: 1272 helix: -0.60 (0.89), residues: 40 sheet: -2.31 (0.45), residues: 84 loop : -1.91 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 410 HIS 0.006 0.002 HIS B 433 PHE 0.023 0.002 PHE B 180 TYR 0.014 0.002 TYR D 37 ARG 0.006 0.001 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 6) link_NAG-ASN : angle 4.13073 ( 18) link_BETA1-4 : bond 0.00759 ( 2) link_BETA1-4 : angle 0.62934 ( 6) link_ALPHA1-3 : bond 0.01834 ( 2) link_ALPHA1-3 : angle 2.56776 ( 6) hydrogen bonds : bond 0.04120 ( 138) hydrogen bonds : angle 6.17407 ( 252) SS BOND : bond 0.00636 ( 52) SS BOND : angle 1.89385 ( 104) link_BETA1-3 : bond 0.00858 ( 2) link_BETA1-3 : angle 4.57517 ( 6) covalent geometry : bond 0.00451 (10276) covalent geometry : angle 0.72933 (13896) *********************** 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 320 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7985 (mm110) cc_final: 0.7522 (mp10) REVERT: A 37 LYS cc_start: 0.8149 (mttt) cc_final: 0.7829 (mttp) REVERT: A 46 ASP cc_start: 0.7339 (m-30) cc_final: 0.6820 (m-30) REVERT: A 54 MET cc_start: 0.7454 (tpp) cc_final: 0.7144 (tpp) REVERT: A 58 CYS cc_start: 0.5246 (t) cc_final: 0.5039 (t) REVERT: A 80 LYS cc_start: 0.7933 (mttt) cc_final: 0.7554 (mtmt) REVERT: A 105 GLN cc_start: 0.8040 (mt0) cc_final: 0.7511 (mt0) REVERT: A 108 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7142 (mmm-85) REVERT: A 139 ASN cc_start: 0.8000 (m110) cc_final: 0.7592 (m-40) REVERT: A 246 SER cc_start: 0.8264 (p) cc_final: 0.8055 (m) REVERT: A 253 LYS cc_start: 0.8044 (mttp) cc_final: 0.7113 (mttp) REVERT: A 255 ARG cc_start: 0.6993 (ttm-80) cc_final: 0.6738 (ttt-90) REVERT: A 268 MET cc_start: 0.7113 (mmt) cc_final: 0.6817 (mmt) REVERT: A 340 ILE cc_start: 0.8071 (mp) cc_final: 0.7731 (mt) REVERT: A 350 SER cc_start: 0.6799 (t) cc_final: 0.6455 (p) REVERT: A 399 LYS cc_start: 0.6886 (mtpp) cc_final: 0.6567 (mtpp) REVERT: A 405 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7109 (tp) REVERT: A 422 ASN cc_start: 0.7792 (m-40) cc_final: 0.7401 (m-40) REVERT: A 436 PHE cc_start: 0.7514 (m-80) cc_final: 0.7301 (m-80) REVERT: A 452 SER cc_start: 0.6969 (p) cc_final: 0.6752 (t) REVERT: A 458 ASP cc_start: 0.7659 (t0) cc_final: 0.7147 (t0) REVERT: A 548 GLU cc_start: 0.4904 (mp0) cc_final: 0.4353 (mp0) REVERT: A 559 HIS cc_start: 0.6668 (t-90) cc_final: 0.6391 (t-90) REVERT: A 574 ARG cc_start: 0.7222 (ptp90) cc_final: 0.6957 (mpp-170) REVERT: A 618 HIS cc_start: 0.6500 (m-70) cc_final: 0.6185 (m-70) REVERT: B 59 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 80 LYS cc_start: 0.8288 (mttt) cc_final: 0.7783 (mttt) REVERT: B 149 ARG cc_start: 0.7044 (ttt90) cc_final: 0.6817 (ttt90) REVERT: B 168 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7648 (p) REVERT: B 171 ASP cc_start: 0.6899 (t0) cc_final: 0.6582 (t0) REVERT: B 253 LYS cc_start: 0.8035 (mttp) cc_final: 0.7735 (mttp) REVERT: B 278 ASP cc_start: 0.7123 (m-30) cc_final: 0.6663 (m-30) REVERT: B 309 ARG cc_start: 0.6817 (mtt180) cc_final: 0.6376 (mmt90) REVERT: B 321 ASP cc_start: 0.6085 (m-30) cc_final: 0.5795 (m-30) REVERT: B 325 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7883 (mmtp) REVERT: B 345 PHE cc_start: 0.7473 (m-10) cc_final: 0.7034 (m-10) REVERT: B 360 LYS cc_start: 0.7903 (tppp) cc_final: 0.7690 (tppp) REVERT: B 364 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8460 (m) REVERT: B 369 LEU cc_start: 0.8278 (mt) cc_final: 0.7892 (mt) REVERT: B 399 LYS cc_start: 0.6914 (mtpp) cc_final: 0.6384 (mtpp) REVERT: B 400 GLU cc_start: 0.7152 (tt0) cc_final: 0.6895 (tt0) REVERT: B 452 SER cc_start: 0.6686 (p) cc_final: 0.5688 (p) REVERT: B 454 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7599 (mmtt) REVERT: B 458 ASP cc_start: 0.7659 (t0) cc_final: 0.7039 (t0) REVERT: B 460 ASP cc_start: 0.6319 (m-30) cc_final: 0.5812 (m-30) REVERT: B 475 ILE cc_start: 0.6727 (mm) cc_final: 0.6510 (mp) REVERT: B 487 LYS cc_start: 0.7137 (pttp) cc_final: 0.6518 (pttp) REVERT: B 521 ARG cc_start: 0.6912 (ppt-90) cc_final: 0.6582 (ppt-90) REVERT: B 618 HIS cc_start: 0.6567 (m-70) cc_final: 0.6321 (m90) outliers start: 22 outliers final: 10 residues processed: 309 average time/residue: 0.2919 time to fit residues: 116.7970 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 : 1.074 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 444 ASN A 493 ASN C 10 HIS C 16 HIS D 10 HIS B 32 GLN B 71 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN B 559 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143063 restraints weight = 15252.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.147467 restraints weight = 7704.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.150433 restraints weight = 4738.976| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10340 Z= 0.205 Angle : 0.771 9.639 14036 Z= 0.380 Chirality : 0.052 0.323 1550 Planarity : 0.005 0.064 1814 Dihedral : 10.235 68.283 1620 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % 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 : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1272 helix: -0.47 (0.92), residues: 42 sheet: -2.36 (0.55), residues: 64 loop : -1.61 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.005 0.001 HIS B 47 PHE 0.015 0.002 PHE B 180 TYR 0.019 0.002 TYR A 125 ARG 0.006 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00769 ( 6) link_NAG-ASN : angle 3.94790 ( 18) link_BETA1-4 : bond 0.00631 ( 2) link_BETA1-4 : angle 1.25721 ( 6) link_ALPHA1-3 : bond 0.02119 ( 2) link_ALPHA1-3 : angle 2.72148 ( 6) hydrogen bonds : bond 0.04110 ( 138) hydrogen bonds : angle 6.21251 ( 252) SS BOND : bond 0.00780 ( 52) SS BOND : angle 1.67658 ( 104) link_BETA1-3 : bond 0.00853 ( 2) link_BETA1-3 : angle 3.46383 ( 6) covalent geometry : bond 0.00434 (10276) covalent geometry : angle 0.74206 (13896) *********************** 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 315 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 1.174 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: 0.8026 (mttt) cc_final: 0.7571 (mttm) REVERT: A 46 ASP cc_start: 0.7416 (m-30) cc_final: 0.6909 (m-30) REVERT: A 59 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 64 ASN cc_start: 0.8309 (m-40) cc_final: 0.7827 (m-40) REVERT: A 80 LYS cc_start: 0.8096 (mttt) cc_final: 0.7583 (mtmt) REVERT: A 83 GLN cc_start: 0.7323 (mt0) cc_final: 0.6769 (mt0) REVERT: A 105 GLN cc_start: 0.8160 (mt0) cc_final: 0.7796 (mt0) REVERT: A 139 ASN cc_start: 0.8120 (m110) cc_final: 0.7673 (m-40) REVERT: A 222 ARG cc_start: 0.5919 (mtp85) cc_final: 0.5486 (mtt90) REVERT: A 235 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6821 (mm-40) REVERT: A 246 SER cc_start: 0.8382 (p) cc_final: 0.8141 (m) REVERT: A 254 PHE cc_start: 0.7658 (m-10) cc_final: 0.7445 (m-80) REVERT: A 335 LYS cc_start: 0.7604 (tptp) cc_final: 0.7247 (tptp) REVERT: A 340 ILE cc_start: 0.8268 (mp) cc_final: 0.7917 (mt) REVERT: A 350 SER cc_start: 0.6964 (t) cc_final: 0.6736 (p) REVERT: A 399 LYS cc_start: 0.7100 (mtpp) cc_final: 0.6755 (mtpp) REVERT: A 405 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6965 (tp) REVERT: A 426 ILE cc_start: 0.8091 (mt) cc_final: 0.7513 (tt) REVERT: A 452 SER cc_start: 0.7179 (p) cc_final: 0.6905 (t) REVERT: A 458 ASP cc_start: 0.7709 (t0) cc_final: 0.7195 (t0) REVERT: A 548 GLU cc_start: 0.4813 (mp0) cc_final: 0.4383 (mp0) REVERT: A 561 GLU cc_start: 0.5873 (tp30) cc_final: 0.2920 (mm-30) REVERT: A 618 HIS cc_start: 0.6697 (m-70) cc_final: 0.6196 (m170) REVERT: B 59 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 66 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6720 (mt-10) REVERT: B 80 LYS cc_start: 0.8315 (mttt) cc_final: 0.7774 (mttt) REVERT: B 149 ARG cc_start: 0.7122 (ttt90) cc_final: 0.6738 (ttt-90) REVERT: B 171 ASP cc_start: 0.6956 (t0) cc_final: 0.6559 (t0) REVERT: B 235 GLN cc_start: 0.7318 (mm-40) cc_final: 0.7086 (mm110) REVERT: B 253 LYS cc_start: 0.7865 (mttp) cc_final: 0.7659 (mttp) REVERT: B 260 CYS cc_start: 0.5667 (OUTLIER) cc_final: 0.4574 (m) REVERT: B 271 ASN cc_start: 0.7897 (t0) cc_final: 0.7337 (m-40) REVERT: B 278 ASP cc_start: 0.7195 (m-30) cc_final: 0.6127 (m-30) REVERT: B 286 SER cc_start: 0.6998 (m) cc_final: 0.6594 (m) REVERT: B 309 ARG cc_start: 0.7344 (mtt180) cc_final: 0.6935 (mtt-85) REVERT: B 345 PHE cc_start: 0.7667 (m-10) cc_final: 0.7386 (m-10) REVERT: B 357 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7825 (ptmm) REVERT: B 364 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8517 (m) REVERT: B 369 LEU cc_start: 0.8423 (mt) cc_final: 0.8091 (mt) REVERT: B 382 THR cc_start: 0.1848 (OUTLIER) cc_final: 0.1619 (m) REVERT: B 399 LYS cc_start: 0.6974 (mtpp) cc_final: 0.6490 (mtpp) REVERT: B 451 ARG cc_start: 0.7311 (ptp90) cc_final: 0.6015 (ptp90) REVERT: B 454 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7663 (mmtt) REVERT: B 458 ASP cc_start: 0.7771 (t0) cc_final: 0.7133 (t0) REVERT: B 460 ASP cc_start: 0.6333 (m-30) cc_final: 0.6116 (m-30) REVERT: B 487 LYS cc_start: 0.7381 (pttp) cc_final: 0.6954 (pttp) REVERT: B 489 LYS cc_start: 0.7267 (ttmt) cc_final: 0.7056 (ttmt) REVERT: B 559 HIS cc_start: 0.6447 (t-90) cc_final: 0.6106 (t-90) REVERT: B 618 HIS cc_start: 0.6936 (m-70) cc_final: 0.6514 (m90) outliers start: 27 outliers final: 11 residues processed: 298 average time/residue: 0.2991 time to fit residues: 116.1473 Evaluate side-chains 292 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 277 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 257 GLU 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 462 ILE 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 4 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 338 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 71 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 466 ASN B 493 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134735 restraints weight = 15043.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138996 restraints weight = 7671.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141872 restraints weight = 4703.690| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 10340 Z= 0.290 Angle : 0.877 17.490 14036 Z= 0.428 Chirality : 0.055 0.328 1550 Planarity : 0.005 0.045 1814 Dihedral : 9.222 64.482 1620 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.86 % Allowed : 12.59 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1272 helix: -0.61 (0.92), residues: 40 sheet: -2.19 (0.57), residues: 74 loop : -1.59 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 49 HIS 0.007 0.002 HIS A 370 PHE 0.030 0.003 PHE B 404 TYR 0.019 0.002 TYR D 37 ARG 0.009 0.001 ARG B 427 Details of bonding type rmsd link_NAG-ASN : bond 0.01180 ( 6) link_NAG-ASN : angle 4.94571 ( 18) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.64095 ( 6) link_ALPHA1-3 : bond 0.02183 ( 2) link_ALPHA1-3 : angle 2.80041 ( 6) hydrogen bonds : bond 0.04216 ( 138) hydrogen bonds : angle 6.55160 ( 252) SS BOND : bond 0.00566 ( 52) SS BOND : angle 1.59256 ( 104) link_BETA1-3 : bond 0.00197 ( 2) link_BETA1-3 : angle 3.22721 ( 6) covalent geometry : bond 0.00625 (10276) covalent geometry : angle 0.84653 (13896) *********************** 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 344 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 312 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8125 (mp10) cc_final: 0.7661 (mt0) REVERT: A 46 ASP cc_start: 0.7333 (m-30) cc_final: 0.6880 (m-30) REVERT: A 54 MET cc_start: 0.7864 (tpp) cc_final: 0.7588 (tpp) REVERT: A 59 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 64 ASN cc_start: 0.8353 (m-40) cc_final: 0.7871 (m-40) REVERT: A 79 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 80 LYS cc_start: 0.8376 (mttt) cc_final: 0.7848 (mttt) REVERT: A 101 LEU cc_start: 0.8456 (mt) cc_final: 0.8242 (mp) REVERT: A 105 GLN cc_start: 0.8273 (mt0) cc_final: 0.7952 (mt0) REVERT: A 139 ASN cc_start: 0.8199 (m110) cc_final: 0.7976 (m-40) REVERT: A 168 VAL cc_start: 0.8547 (t) cc_final: 0.8206 (p) REVERT: A 198 SER cc_start: 0.6148 (m) cc_final: 0.5876 (t) REVERT: A 210 LEU cc_start: 0.8450 (mm) cc_final: 0.8122 (mm) REVERT: A 222 ARG cc_start: 0.6266 (mtp85) cc_final: 0.5876 (mtt90) REVERT: A 252 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7056 (ttp80) REVERT: A 254 PHE cc_start: 0.7793 (m-10) cc_final: 0.7573 (m-80) REVERT: A 299 TYR cc_start: 0.7993 (m-80) cc_final: 0.7538 (m-80) REVERT: A 335 LYS cc_start: 0.7616 (tptp) cc_final: 0.7309 (tptp) REVERT: A 350 SER cc_start: 0.7011 (t) cc_final: 0.6688 (p) REVERT: A 357 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7838 (mtmm) REVERT: A 399 LYS cc_start: 0.7184 (mtpp) cc_final: 0.6802 (mtpp) REVERT: A 405 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6995 (tp) REVERT: A 415 THR cc_start: 0.7515 (p) cc_final: 0.7307 (t) REVERT: A 426 ILE cc_start: 0.8102 (mt) cc_final: 0.7535 (tt) REVERT: A 452 SER cc_start: 0.7329 (p) cc_final: 0.6216 (t) REVERT: A 454 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7678 (mmtt) REVERT: A 458 ASP cc_start: 0.7836 (t0) cc_final: 0.7313 (t0) REVERT: A 460 ASP cc_start: 0.6489 (m-30) cc_final: 0.6171 (m-30) REVERT: A 500 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7440 (mppt) REVERT: A 521 ARG cc_start: 0.7305 (ppt-90) cc_final: 0.6838 (ppt-90) REVERT: A 548 GLU cc_start: 0.5191 (mp0) cc_final: 0.4221 (mp0) REVERT: A 618 HIS cc_start: 0.7126 (m-70) cc_final: 0.6653 (m-70) REVERT: B 32 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7526 (mt0) REVERT: B 59 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 66 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 80 LYS cc_start: 0.8414 (mttt) cc_final: 0.7813 (mttt) REVERT: B 98 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7182 (mtp-110) REVERT: B 106 ILE cc_start: 0.8104 (tt) cc_final: 0.7768 (mp) REVERT: B 111 MET cc_start: 0.7059 (ptm) cc_final: 0.6793 (ptm) REVERT: B 112 TYR cc_start: 0.7565 (m-80) cc_final: 0.6681 (m-80) REVERT: B 139 ASN cc_start: 0.7874 (m110) cc_final: 0.7630 (m-40) REVERT: B 149 ARG cc_start: 0.7288 (ttt90) cc_final: 0.6952 (ttt-90) REVERT: B 168 VAL cc_start: 0.8176 (t) cc_final: 0.7908 (p) REVERT: B 171 ASP cc_start: 0.7130 (t0) cc_final: 0.6581 (t0) REVERT: B 172 PHE cc_start: 0.8072 (m-10) cc_final: 0.7463 (m-10) REVERT: B 235 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6502 (mm-40) REVERT: B 260 CYS cc_start: 0.6051 (OUTLIER) cc_final: 0.4959 (m) REVERT: B 271 ASN cc_start: 0.7923 (t0) cc_final: 0.7413 (m-40) REVERT: B 285 TYR cc_start: 0.7656 (m-80) cc_final: 0.7309 (m-80) REVERT: B 286 SER cc_start: 0.7272 (m) cc_final: 0.6907 (m) REVERT: B 364 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 369 LEU cc_start: 0.8485 (mt) cc_final: 0.8214 (mt) REVERT: B 374 VAL cc_start: 0.8088 (m) cc_final: 0.7740 (t) REVERT: B 382 THR cc_start: 0.2751 (OUTLIER) cc_final: 0.2400 (m) REVERT: B 396 LYS cc_start: 0.7796 (mttt) cc_final: 0.7177 (mttm) REVERT: B 399 LYS cc_start: 0.7173 (mtpp) cc_final: 0.6703 (mtpp) REVERT: B 415 THR cc_start: 0.7737 (p) cc_final: 0.7408 (t) REVERT: B 454 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7688 (mmtt) REVERT: B 458 ASP cc_start: 0.7856 (t0) cc_final: 0.7399 (t0) REVERT: B 487 LYS cc_start: 0.7722 (pttp) cc_final: 0.7286 (pttp) REVERT: B 489 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7273 (ttmt) REVERT: B 502 THR cc_start: 0.8155 (p) cc_final: 0.7883 (t) REVERT: B 559 HIS cc_start: 0.6807 (t-90) cc_final: 0.6554 (t-90) REVERT: B 581 GLN cc_start: 0.7662 (tt0) cc_final: 0.7330 (tm-30) REVERT: B 618 HIS cc_start: 0.7109 (m-70) cc_final: 0.6767 (m90) outliers start: 32 outliers final: 16 residues processed: 324 average time/residue: 0.2803 time to fit residues: 118.9684 Evaluate side-chains 319 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 297 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 500 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 72 ARG Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 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 103 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 358 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132782 restraints weight = 15245.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137173 restraints weight = 7628.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140018 restraints weight = 4641.323| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10340 Z= 0.205 Angle : 0.774 10.122 14036 Z= 0.382 Chirality : 0.051 0.341 1550 Planarity : 0.005 0.069 1814 Dihedral : 8.426 57.792 1620 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.68 % Allowed : 15.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.23), residues: 1272 helix: -0.91 (0.87), residues: 40 sheet: -2.09 (0.67), residues: 54 loop : -1.41 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 49 HIS 0.007 0.001 HIS A 418 PHE 0.026 0.002 PHE B 48 TYR 0.019 0.002 TYR B 471 ARG 0.010 0.001 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 6) link_NAG-ASN : angle 4.73657 ( 18) link_BETA1-4 : bond 0.00663 ( 2) link_BETA1-4 : angle 1.96993 ( 6) link_ALPHA1-3 : bond 0.02439 ( 2) link_ALPHA1-3 : angle 3.16806 ( 6) hydrogen bonds : bond 0.03994 ( 138) hydrogen bonds : angle 6.36498 ( 252) SS BOND : bond 0.00463 ( 52) SS BOND : angle 1.63878 ( 104) link_BETA1-3 : bond 0.00601 ( 2) link_BETA1-3 : angle 2.81118 ( 6) covalent geometry : bond 0.00452 (10276) covalent geometry : angle 0.73946 (13896) *********************** 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 325 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8009 (mp-120) cc_final: 0.7803 (mm-40) REVERT: A 54 MET cc_start: 0.7889 (tpp) cc_final: 0.7464 (tpp) REVERT: A 59 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 79 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 80 LYS cc_start: 0.8353 (mttt) cc_final: 0.7799 (mttt) REVERT: A 101 LEU cc_start: 0.8481 (mt) cc_final: 0.8266 (mp) REVERT: A 125 TYR cc_start: 0.7862 (p90) cc_final: 0.7468 (p90) REVERT: A 168 VAL cc_start: 0.8491 (t) cc_final: 0.8177 (p) REVERT: A 210 LEU cc_start: 0.8421 (mm) cc_final: 0.8184 (mm) REVERT: A 222 ARG cc_start: 0.6427 (mtp85) cc_final: 0.6060 (mtt90) REVERT: A 335 LYS cc_start: 0.7564 (tptp) cc_final: 0.7284 (tptp) REVERT: A 350 SER cc_start: 0.7088 (t) cc_final: 0.6747 (p) REVERT: A 357 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7790 (mtmm) REVERT: A 399 LYS cc_start: 0.7142 (mtpp) cc_final: 0.6791 (mtpp) REVERT: A 405 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7163 (tp) REVERT: A 415 THR cc_start: 0.7540 (p) cc_final: 0.7310 (t) REVERT: A 426 ILE cc_start: 0.8096 (mt) cc_final: 0.7552 (tt) REVERT: A 452 SER cc_start: 0.7417 (p) cc_final: 0.6279 (t) REVERT: A 454 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7594 (mmtt) REVERT: A 458 ASP cc_start: 0.7854 (t0) cc_final: 0.7354 (t0) REVERT: A 460 ASP cc_start: 0.6411 (m-30) cc_final: 0.5897 (m-30) REVERT: A 500 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7346 (mptt) REVERT: A 521 ARG cc_start: 0.7375 (ppt-90) cc_final: 0.7144 (ptt-90) REVERT: A 618 HIS cc_start: 0.7073 (m-70) cc_final: 0.6479 (m170) REVERT: B 32 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: B 54 MET cc_start: 0.7960 (tpp) cc_final: 0.7370 (tpp) REVERT: B 59 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 66 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6431 (mt-10) REVERT: B 80 LYS cc_start: 0.8389 (mttt) cc_final: 0.7791 (mttt) REVERT: B 134 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6496 (mm-30) REVERT: B 149 ARG cc_start: 0.7362 (ttt90) cc_final: 0.6914 (ttt-90) REVERT: B 163 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7693 (tm-30) REVERT: B 168 VAL cc_start: 0.8141 (t) cc_final: 0.7834 (p) REVERT: B 171 ASP cc_start: 0.7172 (t0) cc_final: 0.6598 (t0) REVERT: B 172 PHE cc_start: 0.7998 (m-10) cc_final: 0.7448 (m-10) REVERT: B 210 LEU cc_start: 0.8438 (mm) cc_final: 0.7872 (tp) REVERT: B 235 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6468 (mm-40) REVERT: B 252 ARG cc_start: 0.7222 (ttt-90) cc_final: 0.6647 (ttp80) REVERT: B 260 CYS cc_start: 0.6147 (OUTLIER) cc_final: 0.4455 (m) REVERT: B 261 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7282 (mmtt) REVERT: B 263 THR cc_start: 0.8521 (m) cc_final: 0.8223 (p) REVERT: B 271 ASN cc_start: 0.7922 (t0) cc_final: 0.7410 (m-40) REVERT: B 286 SER cc_start: 0.7175 (m) cc_final: 0.6915 (m) REVERT: B 309 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7488 (mtm-85) REVERT: B 350 SER cc_start: 0.7007 (t) cc_final: 0.6713 (p) REVERT: B 364 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8539 (m) REVERT: B 369 LEU cc_start: 0.8422 (mt) cc_final: 0.8118 (mt) REVERT: B 382 THR cc_start: 0.2964 (OUTLIER) cc_final: 0.2683 (m) REVERT: B 396 LYS cc_start: 0.7799 (mttt) cc_final: 0.7128 (mttm) REVERT: B 399 LYS cc_start: 0.7050 (mtpp) cc_final: 0.6637 (mtpp) REVERT: B 427 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7951 (mmt90) REVERT: B 454 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7672 (mmtt) REVERT: B 458 ASP cc_start: 0.7826 (t0) cc_final: 0.7356 (t0) REVERT: B 487 LYS cc_start: 0.7751 (pttp) cc_final: 0.7451 (pttp) REVERT: B 502 THR cc_start: 0.8254 (p) cc_final: 0.8009 (t) REVERT: B 534 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6746 (mp0) REVERT: B 618 HIS cc_start: 0.7010 (m-70) cc_final: 0.6608 (m90) outliers start: 30 outliers final: 15 residues processed: 306 average time/residue: 0.2955 time to fit residues: 117.2813 Evaluate side-chains 311 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain B residue 32 GLN 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 260 CYS 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 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 69 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 41 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4005 r_free = 0.4005 target = 0.156263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131622 restraints weight = 15030.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136036 restraints weight = 7542.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138974 restraints weight = 4553.563| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10340 Z= 0.211 Angle : 0.783 9.834 14036 Z= 0.383 Chirality : 0.051 0.328 1550 Planarity : 0.004 0.066 1814 Dihedral : 8.055 55.222 1620 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.50 % Allowed : 16.88 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.23), residues: 1272 helix: -1.16 (0.84), residues: 40 sheet: -2.08 (0.68), residues: 54 loop : -1.29 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 49 HIS 0.005 0.001 HIS B 559 PHE 0.027 0.002 PHE A 172 TYR 0.028 0.002 TYR B 471 ARG 0.019 0.001 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 6) link_NAG-ASN : angle 4.79099 ( 18) link_BETA1-4 : bond 0.00661 ( 2) link_BETA1-4 : angle 1.90835 ( 6) link_ALPHA1-3 : bond 0.02505 ( 2) link_ALPHA1-3 : angle 3.30530 ( 6) hydrogen bonds : bond 0.03953 ( 138) hydrogen bonds : angle 6.38051 ( 252) SS BOND : bond 0.00460 ( 52) SS BOND : angle 1.55321 ( 104) link_BETA1-3 : bond 0.00435 ( 2) link_BETA1-3 : angle 2.76363 ( 6) covalent geometry : bond 0.00456 (10276) covalent geometry : angle 0.74908 (13896) *********************** 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 339 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 1.208 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: 0.7945 (mp-120) cc_final: 0.7744 (mm-40) REVERT: A 59 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 80 LYS cc_start: 0.8403 (mttt) cc_final: 0.7810 (mttt) REVERT: A 83 GLN cc_start: 0.7293 (mt0) cc_final: 0.6692 (mt0) REVERT: A 125 TYR cc_start: 0.7903 (p90) cc_final: 0.7609 (p90) REVERT: A 168 VAL cc_start: 0.8488 (t) cc_final: 0.8191 (p) REVERT: A 171 ASP cc_start: 0.6729 (t0) cc_final: 0.6404 (t0) REVERT: A 172 PHE cc_start: 0.8025 (m-10) cc_final: 0.7495 (m-10) REVERT: A 198 SER cc_start: 0.6386 (m) cc_final: 0.6158 (t) REVERT: A 210 LEU cc_start: 0.8524 (mm) cc_final: 0.8245 (mm) REVERT: A 255 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6760 (ttt-90) REVERT: A 256 ASP cc_start: 0.6683 (m-30) cc_final: 0.6465 (m-30) REVERT: A 335 LYS cc_start: 0.7526 (tptp) cc_final: 0.7268 (tptp) REVERT: A 350 SER cc_start: 0.7150 (t) cc_final: 0.6849 (p) REVERT: A 357 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7778 (mtmm) REVERT: A 399 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6819 (mtpp) REVERT: A 405 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7182 (tp) REVERT: A 415 THR cc_start: 0.7613 (p) cc_final: 0.7252 (t) REVERT: A 426 ILE cc_start: 0.8131 (mt) cc_final: 0.7528 (tt) REVERT: A 451 ARG cc_start: 0.7377 (ptp90) cc_final: 0.6912 (ptp90) REVERT: A 452 SER cc_start: 0.7429 (p) cc_final: 0.6886 (t) REVERT: A 454 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7622 (mmtt) REVERT: A 458 ASP cc_start: 0.7842 (t0) cc_final: 0.7428 (t0) REVERT: A 460 ASP cc_start: 0.6491 (m-30) cc_final: 0.6074 (m-30) REVERT: A 489 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7541 (mtmt) REVERT: A 500 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7292 (mptt) REVERT: A 521 ARG cc_start: 0.7510 (ppt-90) cc_final: 0.7033 (ptt-90) REVERT: A 548 GLU cc_start: 0.5367 (mp0) cc_final: 0.5098 (mp0) REVERT: A 561 GLU cc_start: 0.5646 (tp30) cc_final: 0.4782 (mm-30) REVERT: A 586 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6798 (tp) REVERT: A 618 HIS cc_start: 0.7226 (m-70) cc_final: 0.6627 (m170) REVERT: B 32 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: B 54 MET cc_start: 0.7956 (tpp) cc_final: 0.7388 (tpp) REVERT: B 59 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 66 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6206 (mt-10) REVERT: B 80 LYS cc_start: 0.8425 (mttt) cc_final: 0.7800 (mttt) REVERT: B 106 ILE cc_start: 0.8104 (tt) cc_final: 0.7723 (mp) REVERT: B 134 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6620 (mm-30) REVERT: B 149 ARG cc_start: 0.7382 (ttt90) cc_final: 0.6883 (ttt-90) REVERT: B 168 VAL cc_start: 0.8220 (t) cc_final: 0.7890 (p) REVERT: B 171 ASP cc_start: 0.7273 (t0) cc_final: 0.6663 (t0) REVERT: B 172 PHE cc_start: 0.8001 (m-10) cc_final: 0.7472 (m-10) REVERT: B 210 LEU cc_start: 0.8436 (mm) cc_final: 0.7853 (tp) REVERT: B 235 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6476 (mm-40) REVERT: B 252 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6791 (ttp80) REVERT: B 255 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6421 (ttm-80) REVERT: B 260 CYS cc_start: 0.6192 (OUTLIER) cc_final: 0.4073 (m) REVERT: B 261 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7302 (mmtt) REVERT: B 263 THR cc_start: 0.8530 (m) cc_final: 0.8155 (p) REVERT: B 271 ASN cc_start: 0.7946 (t0) cc_final: 0.7269 (m-40) REVERT: B 286 SER cc_start: 0.7214 (m) cc_final: 0.6962 (m) REVERT: B 364 SER cc_start: 0.8888 (p) cc_final: 0.8518 (m) REVERT: B 369 LEU cc_start: 0.8388 (mt) cc_final: 0.8054 (mt) REVERT: B 382 THR cc_start: 0.3320 (OUTLIER) cc_final: 0.3050 (m) REVERT: B 396 LYS cc_start: 0.7733 (mttt) cc_final: 0.7303 (mttm) REVERT: B 399 LYS cc_start: 0.7113 (mtpp) cc_final: 0.6633 (mtpp) REVERT: B 415 THR cc_start: 0.7681 (p) cc_final: 0.7171 (t) REVERT: B 427 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7924 (mmt90) REVERT: B 454 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7654 (mmtt) REVERT: B 458 ASP cc_start: 0.7859 (t0) cc_final: 0.7346 (t0) REVERT: B 487 LYS cc_start: 0.7854 (pttp) cc_final: 0.7494 (pttp) REVERT: B 502 THR cc_start: 0.8279 (p) cc_final: 0.8059 (t) REVERT: B 533 ARG cc_start: 0.6787 (tpm170) cc_final: 0.6534 (tpm170) REVERT: B 534 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6887 (mp0) REVERT: B 618 HIS cc_start: 0.7047 (m-70) cc_final: 0.6644 (m90) outliers start: 28 outliers final: 15 residues processed: 326 average time/residue: 0.2892 time to fit residues: 122.0544 Evaluate side-chains 321 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 153 ASN 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 405 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 536 VAL 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 83 GLN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 420 PHE 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 117 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 121 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.157991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133605 restraints weight = 15327.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138034 restraints weight = 7836.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140989 restraints weight = 4799.235| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10340 Z= 0.170 Angle : 0.774 9.977 14036 Z= 0.376 Chirality : 0.050 0.340 1550 Planarity : 0.004 0.045 1814 Dihedral : 7.676 55.554 1620 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.86 % Allowed : 18.12 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1272 helix: -1.16 (0.85), residues: 40 sheet: -1.97 (0.69), residues: 54 loop : -1.21 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 49 HIS 0.004 0.001 HIS B 559 PHE 0.017 0.002 PHE B 404 TYR 0.020 0.002 TYR C 37 ARG 0.010 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 6) link_NAG-ASN : angle 4.70801 ( 18) link_BETA1-4 : bond 0.00721 ( 2) link_BETA1-4 : angle 2.12750 ( 6) link_ALPHA1-3 : bond 0.02456 ( 2) link_ALPHA1-3 : angle 3.51796 ( 6) hydrogen bonds : bond 0.03859 ( 138) hydrogen bonds : angle 6.23109 ( 252) SS BOND : bond 0.00471 ( 52) SS BOND : angle 1.45298 ( 104) link_BETA1-3 : bond 0.00705 ( 2) link_BETA1-3 : angle 2.85857 ( 6) covalent geometry : bond 0.00372 (10276) covalent geometry : angle 0.74146 (13896) *********************** 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 342 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 1.043 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: 0.7907 (mp-120) cc_final: 0.7256 (mp-120) REVERT: A 54 MET cc_start: 0.7766 (tpp) cc_final: 0.7111 (tpp) REVERT: A 59 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 80 LYS cc_start: 0.8077 (mttt) cc_final: 0.7547 (mttt) REVERT: A 83 GLN cc_start: 0.7274 (mt0) cc_final: 0.6654 (mt0) REVERT: A 124 ASN cc_start: 0.8058 (m-40) cc_final: 0.7844 (m-40) REVERT: A 125 TYR cc_start: 0.7858 (p90) cc_final: 0.7616 (p90) REVERT: A 168 VAL cc_start: 0.8435 (t) cc_final: 0.8171 (p) REVERT: A 171 ASP cc_start: 0.6681 (t0) cc_final: 0.6439 (t0) REVERT: A 172 PHE cc_start: 0.7937 (m-10) cc_final: 0.7436 (m-10) REVERT: A 210 LEU cc_start: 0.8456 (mm) cc_final: 0.8207 (mm) REVERT: A 255 ARG cc_start: 0.6926 (ttm-80) cc_final: 0.6673 (ttt-90) REVERT: A 260 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.5030 (m) REVERT: A 335 LYS cc_start: 0.7503 (tptp) cc_final: 0.7259 (tptp) REVERT: A 350 SER cc_start: 0.7190 (t) cc_final: 0.6904 (p) REVERT: A 357 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7776 (mtmm) REVERT: A 399 LYS cc_start: 0.7207 (mtpp) cc_final: 0.6824 (mtpp) REVERT: A 405 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7272 (tp) REVERT: A 415 THR cc_start: 0.7612 (p) cc_final: 0.7209 (t) REVERT: A 426 ILE cc_start: 0.8162 (mt) cc_final: 0.7568 (tt) REVERT: A 452 SER cc_start: 0.7436 (p) cc_final: 0.6891 (t) REVERT: A 454 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7641 (mmtt) REVERT: A 458 ASP cc_start: 0.7824 (t0) cc_final: 0.7394 (t0) REVERT: A 467 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6930 (mmtm) REVERT: A 489 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7579 (mtmt) REVERT: A 522 ASP cc_start: 0.6975 (m-30) cc_final: 0.5940 (t0) REVERT: A 548 GLU cc_start: 0.4978 (mp0) cc_final: 0.4750 (mp0) REVERT: A 561 GLU cc_start: 0.5932 (tp30) cc_final: 0.5099 (mm-30) REVERT: A 586 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6661 (tp) REVERT: A 618 HIS cc_start: 0.6996 (m-70) cc_final: 0.6654 (m-70) REVERT: D 37 TYR cc_start: 0.8408 (m-10) cc_final: 0.8151 (m-10) REVERT: B 32 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: B 54 MET cc_start: 0.7930 (tpp) cc_final: 0.7248 (tpp) REVERT: B 59 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 66 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: B 80 LYS cc_start: 0.8378 (mttt) cc_final: 0.7767 (mttt) REVERT: B 98 ARG cc_start: 0.7693 (ttt90) cc_final: 0.7350 (mtp85) REVERT: B 149 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6886 (ttt-90) REVERT: B 168 VAL cc_start: 0.8267 (t) cc_final: 0.7892 (p) REVERT: B 171 ASP cc_start: 0.7284 (t0) cc_final: 0.6758 (t0) REVERT: B 172 PHE cc_start: 0.7884 (m-10) cc_final: 0.7353 (m-10) REVERT: B 210 LEU cc_start: 0.8402 (mm) cc_final: 0.7803 (tp) REVERT: B 235 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6892 (mm-40) REVERT: B 261 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7198 (mmtt) REVERT: B 263 THR cc_start: 0.8491 (m) cc_final: 0.8203 (p) REVERT: B 278 ASP cc_start: 0.7381 (m-30) cc_final: 0.6936 (m-30) REVERT: B 286 SER cc_start: 0.7224 (m) cc_final: 0.6939 (m) REVERT: B 309 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7481 (mtm-85) REVERT: B 340 ILE cc_start: 0.8045 (mm) cc_final: 0.7804 (mm) REVERT: B 364 SER cc_start: 0.8889 (p) cc_final: 0.8553 (m) REVERT: B 370 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7641 (m170) REVERT: B 382 THR cc_start: 0.3225 (OUTLIER) cc_final: 0.2929 (m) REVERT: B 396 LYS cc_start: 0.7759 (mttt) cc_final: 0.6742 (mtpp) REVERT: B 399 LYS cc_start: 0.7149 (mtpp) cc_final: 0.6695 (mtpp) REVERT: B 415 THR cc_start: 0.7652 (p) cc_final: 0.7136 (t) REVERT: B 454 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7662 (mmtt) REVERT: B 458 ASP cc_start: 0.7850 (t0) cc_final: 0.7389 (t0) REVERT: B 487 LYS cc_start: 0.7861 (pttp) cc_final: 0.7480 (pttp) REVERT: B 502 THR cc_start: 0.8323 (p) cc_final: 0.8069 (t) REVERT: B 534 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6883 (mp0) REVERT: B 561 GLU cc_start: 0.6820 (tp30) cc_final: 0.6179 (tp30) REVERT: B 565 GLN cc_start: 0.6656 (mp10) cc_final: 0.6291 (mp10) REVERT: B 618 HIS cc_start: 0.6935 (m-70) cc_final: 0.6583 (m90) outliers start: 32 outliers final: 17 residues processed: 327 average time/residue: 0.2949 time to fit residues: 124.3227 Evaluate side-chains 331 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 536 VAL 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 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 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 420 PHE 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 55 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 466 ASN ** 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 235 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131416 restraints weight = 15101.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135747 restraints weight = 7722.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138665 restraints weight = 4748.690| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10340 Z= 0.201 Angle : 0.804 10.277 14036 Z= 0.393 Chirality : 0.051 0.330 1550 Planarity : 0.004 0.060 1814 Dihedral : 7.565 55.243 1620 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 2.77 % Allowed : 18.57 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1272 helix: -1.07 (0.86), residues: 38 sheet: -1.80 (0.68), residues: 54 loop : -1.15 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 49 HIS 0.006 0.001 HIS B 559 PHE 0.026 0.002 PHE A 404 TYR 0.023 0.002 TYR A 117 ARG 0.010 0.001 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 6) link_NAG-ASN : angle 4.87957 ( 18) link_BETA1-4 : bond 0.00700 ( 2) link_BETA1-4 : angle 2.08676 ( 6) link_ALPHA1-3 : bond 0.02481 ( 2) link_ALPHA1-3 : angle 3.60814 ( 6) hydrogen bonds : bond 0.04015 ( 138) hydrogen bonds : angle 6.29304 ( 252) SS BOND : bond 0.00496 ( 52) SS BOND : angle 1.50521 ( 104) link_BETA1-3 : bond 0.00373 ( 2) link_BETA1-3 : angle 2.97959 ( 6) covalent geometry : bond 0.00438 (10276) covalent geometry : angle 0.77084 (13896) *********************** 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 341 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 310 time to evaluate : 1.016 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 59 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 80 LYS cc_start: 0.8212 (mttt) cc_final: 0.7631 (mttt) REVERT: A 83 GLN cc_start: 0.7286 (mt0) cc_final: 0.6704 (mt0) REVERT: A 149 ARG cc_start: 0.7146 (mtp-110) cc_final: 0.6934 (mtp85) REVERT: A 168 VAL cc_start: 0.8427 (t) cc_final: 0.8179 (p) REVERT: A 210 LEU cc_start: 0.8499 (mm) cc_final: 0.8235 (mm) REVERT: A 252 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.6962 (mtp-110) REVERT: A 335 LYS cc_start: 0.7456 (tptp) cc_final: 0.7227 (tptp) REVERT: A 350 SER cc_start: 0.7221 (t) cc_final: 0.6926 (p) REVERT: A 357 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 361 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6577 (t0) REVERT: A 399 LYS cc_start: 0.7214 (mtpp) cc_final: 0.6834 (mtpp) REVERT: A 405 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7247 (tp) REVERT: A 426 ILE cc_start: 0.8181 (mt) cc_final: 0.7589 (tt) REVERT: A 452 SER cc_start: 0.7507 (p) cc_final: 0.6940 (t) REVERT: A 454 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7637 (mmtt) REVERT: A 458 ASP cc_start: 0.7824 (t0) cc_final: 0.7293 (t0) REVERT: A 521 ARG cc_start: 0.7464 (ppt-90) cc_final: 0.6891 (ppt-90) REVERT: A 548 GLU cc_start: 0.5187 (mp0) cc_final: 0.4877 (mp0) REVERT: A 561 GLU cc_start: 0.5809 (tp30) cc_final: 0.4594 (tp30) REVERT: A 565 GLN cc_start: 0.5950 (mp10) cc_final: 0.5675 (mp10) REVERT: A 586 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6589 (tp) REVERT: A 600 MET cc_start: 0.6286 (tpp) cc_final: 0.5714 (tpp) REVERT: A 618 HIS cc_start: 0.7213 (m-70) cc_final: 0.6767 (m170) REVERT: B 54 MET cc_start: 0.7753 (tpp) cc_final: 0.7039 (tpp) REVERT: B 59 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7216 (mt-10) REVERT: B 66 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6195 (mt-10) REVERT: B 80 LYS cc_start: 0.8401 (mttt) cc_final: 0.7777 (mttt) REVERT: B 149 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7003 (ttt90) REVERT: B 168 VAL cc_start: 0.8267 (t) cc_final: 0.7882 (p) REVERT: B 171 ASP cc_start: 0.7363 (t0) cc_final: 0.6825 (t0) REVERT: B 172 PHE cc_start: 0.7876 (m-10) cc_final: 0.7341 (m-10) REVERT: B 210 LEU cc_start: 0.8345 (mm) cc_final: 0.7810 (tp) REVERT: B 235 GLN cc_start: 0.7461 (mm110) cc_final: 0.6936 (mm110) REVERT: B 252 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6982 (ttp-110) REVERT: B 260 CYS cc_start: 0.6251 (OUTLIER) cc_final: 0.3480 (t) REVERT: B 261 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7147 (mmtt) REVERT: B 263 THR cc_start: 0.8412 (m) cc_final: 0.8134 (p) REVERT: B 278 ASP cc_start: 0.7373 (m-30) cc_final: 0.6966 (m-30) REVERT: B 286 SER cc_start: 0.7290 (m) cc_final: 0.7012 (m) REVERT: B 364 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8543 (m) REVERT: B 368 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: B 370 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7869 (m170) REVERT: B 382 THR cc_start: 0.3621 (OUTLIER) cc_final: 0.3319 (m) REVERT: B 399 LYS cc_start: 0.7045 (mtpp) cc_final: 0.6599 (mtpp) REVERT: B 404 PHE cc_start: 0.7946 (p90) cc_final: 0.7561 (p90) REVERT: B 408 GLN cc_start: 0.7964 (tt0) cc_final: 0.7685 (mt0) REVERT: B 427 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7935 (mmt90) REVERT: B 454 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7682 (mmtt) REVERT: B 458 ASP cc_start: 0.7898 (t0) cc_final: 0.7461 (t0) REVERT: B 487 LYS cc_start: 0.7871 (pttp) cc_final: 0.7482 (pttp) REVERT: B 502 THR cc_start: 0.8361 (p) cc_final: 0.8103 (t) REVERT: B 522 ASP cc_start: 0.6637 (m-30) cc_final: 0.5877 (m-30) REVERT: B 618 HIS cc_start: 0.7023 (m-70) cc_final: 0.6632 (m90) outliers start: 31 outliers final: 15 residues processed: 322 average time/residue: 0.2788 time to fit residues: 116.9852 Evaluate side-chains 325 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 361 ASN 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 569 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 26 LEU 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 153 ASN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 538 LYS 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 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 116 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131125 restraints weight = 15181.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135471 restraints weight = 7785.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138384 restraints weight = 4795.284| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10340 Z= 0.189 Angle : 0.808 10.782 14036 Z= 0.393 Chirality : 0.051 0.337 1550 Planarity : 0.004 0.061 1814 Dihedral : 7.479 54.942 1620 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 1.88 % Allowed : 20.54 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1272 helix: -1.13 (0.86), residues: 38 sheet: -1.85 (0.68), residues: 54 loop : -1.16 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 49 HIS 0.007 0.001 HIS A 433 PHE 0.032 0.002 PHE A 172 TYR 0.023 0.002 TYR D 37 ARG 0.009 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 6) link_NAG-ASN : angle 4.89161 ( 18) link_BETA1-4 : bond 0.00725 ( 2) link_BETA1-4 : angle 2.17726 ( 6) link_ALPHA1-3 : bond 0.02537 ( 2) link_ALPHA1-3 : angle 3.70112 ( 6) hydrogen bonds : bond 0.03925 ( 138) hydrogen bonds : angle 6.22047 ( 252) SS BOND : bond 0.00441 ( 52) SS BOND : angle 1.59188 ( 104) link_BETA1-3 : bond 0.00477 ( 2) link_BETA1-3 : angle 3.00192 ( 6) covalent geometry : bond 0.00413 (10276) covalent geometry : angle 0.77285 (13896) *********************** 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 327 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7779 (tpp) cc_final: 0.6894 (tpp) REVERT: A 59 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 80 LYS cc_start: 0.8173 (mttt) cc_final: 0.7585 (mttt) REVERT: A 83 GLN cc_start: 0.7285 (mt0) cc_final: 0.6677 (mt0) REVERT: A 165 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7747 (ttt180) REVERT: A 168 VAL cc_start: 0.8408 (t) cc_final: 0.8160 (p) REVERT: A 210 LEU cc_start: 0.8413 (mm) cc_final: 0.8140 (mm) REVERT: A 252 ARG cc_start: 0.7248 (mtp-110) cc_final: 0.6959 (mtp-110) REVERT: A 335 LYS cc_start: 0.7439 (tptp) cc_final: 0.7218 (tptp) REVERT: A 350 SER cc_start: 0.7211 (t) cc_final: 0.6936 (p) REVERT: A 357 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7767 (mtmm) REVERT: A 399 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6826 (mtpp) REVERT: A 405 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7241 (tp) REVERT: A 415 THR cc_start: 0.7573 (p) cc_final: 0.7216 (t) REVERT: A 426 ILE cc_start: 0.8182 (mt) cc_final: 0.7582 (tt) REVERT: A 452 SER cc_start: 0.7576 (p) cc_final: 0.6854 (t) REVERT: A 454 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7560 (mmtt) REVERT: A 458 ASP cc_start: 0.7787 (t0) cc_final: 0.7475 (t0) REVERT: A 521 ARG cc_start: 0.7443 (ppt-90) cc_final: 0.6862 (ppt-90) REVERT: A 548 GLU cc_start: 0.5094 (mp0) cc_final: 0.4591 (mp0) REVERT: A 561 GLU cc_start: 0.5774 (tp30) cc_final: 0.4277 (tp30) REVERT: A 565 GLN cc_start: 0.5874 (mp10) cc_final: 0.5656 (mp10) REVERT: A 586 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6542 (tp) REVERT: A 600 MET cc_start: 0.6306 (tpp) cc_final: 0.5749 (tpp) REVERT: A 618 HIS cc_start: 0.7153 (m-70) cc_final: 0.6910 (m-70) REVERT: C 49 TRP cc_start: 0.7650 (m-10) cc_final: 0.7305 (m-10) REVERT: D 37 TYR cc_start: 0.8450 (m-10) cc_final: 0.8209 (m-10) REVERT: B 32 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 54 MET cc_start: 0.7637 (tpp) cc_final: 0.6902 (tpp) REVERT: B 59 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7258 (mt-10) REVERT: B 66 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6165 (mt-10) REVERT: B 80 LYS cc_start: 0.8386 (mttt) cc_final: 0.7743 (mttt) REVERT: B 98 ARG cc_start: 0.7795 (ttt90) cc_final: 0.7394 (mmm-85) REVERT: B 149 ARG cc_start: 0.7415 (ttt90) cc_final: 0.6826 (ttt-90) REVERT: B 168 VAL cc_start: 0.8261 (t) cc_final: 0.7885 (p) REVERT: B 171 ASP cc_start: 0.7326 (t0) cc_final: 0.7007 (t0) REVERT: B 210 LEU cc_start: 0.8342 (mm) cc_final: 0.7788 (tp) REVERT: B 235 GLN cc_start: 0.7452 (mm110) cc_final: 0.6944 (mm-40) REVERT: B 252 ARG cc_start: 0.7159 (ttp80) cc_final: 0.6958 (ttp80) REVERT: B 261 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7230 (mmtt) REVERT: B 263 THR cc_start: 0.8401 (m) cc_final: 0.8151 (p) REVERT: B 278 ASP cc_start: 0.7374 (m-30) cc_final: 0.6966 (m-30) REVERT: B 286 SER cc_start: 0.7317 (m) cc_final: 0.7008 (m) REVERT: B 309 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7552 (mtm-85) REVERT: B 364 SER cc_start: 0.8867 (p) cc_final: 0.8563 (m) REVERT: B 368 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: B 370 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7833 (m170) REVERT: B 382 THR cc_start: 0.3779 (OUTLIER) cc_final: 0.3505 (m) REVERT: B 399 LYS cc_start: 0.7064 (mtpp) cc_final: 0.6635 (mtpp) REVERT: B 404 PHE cc_start: 0.7980 (p90) cc_final: 0.7517 (p90) REVERT: B 454 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7651 (mmtt) REVERT: B 458 ASP cc_start: 0.7890 (t0) cc_final: 0.7456 (t0) REVERT: B 487 LYS cc_start: 0.7842 (pttp) cc_final: 0.7462 (pttp) REVERT: B 502 THR cc_start: 0.8375 (p) cc_final: 0.8138 (t) REVERT: B 522 ASP cc_start: 0.6660 (m-30) cc_final: 0.6206 (m-30) REVERT: B 534 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6587 (mp0) REVERT: B 561 GLU cc_start: 0.6433 (tp30) cc_final: 0.6123 (tp30) REVERT: B 618 HIS cc_start: 0.7090 (m-70) cc_final: 0.6703 (m90) outliers start: 21 outliers final: 13 residues processed: 314 average time/residue: 0.2740 time to fit residues: 112.1965 Evaluate side-chains 319 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 249 LEU 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 586 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 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 209 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 420 PHE 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 113 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 120 optimal weight: 0.0060 chunk 89 optimal weight: 0.5980 chunk 111 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.159248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134888 restraints weight = 15108.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139280 restraints weight = 7754.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142196 restraints weight = 4753.901| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10340 Z= 0.130 Angle : 0.778 10.937 14036 Z= 0.376 Chirality : 0.050 0.345 1550 Planarity : 0.004 0.054 1814 Dihedral : 7.160 55.069 1620 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 1.52 % Allowed : 21.34 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1272 helix: -1.37 (0.84), residues: 40 sheet: -1.80 (0.69), residues: 54 loop : -1.05 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 49 HIS 0.006 0.001 HIS A 433 PHE 0.030 0.002 PHE A 172 TYR 0.019 0.001 TYR D 22 ARG 0.008 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 6) link_NAG-ASN : angle 4.58081 ( 18) link_BETA1-4 : bond 0.00900 ( 2) link_BETA1-4 : angle 2.20207 ( 6) link_ALPHA1-3 : bond 0.02646 ( 2) link_ALPHA1-3 : angle 3.95954 ( 6) hydrogen bonds : bond 0.03471 ( 138) hydrogen bonds : angle 6.08250 ( 252) SS BOND : bond 0.00336 ( 52) SS BOND : angle 1.41817 ( 104) link_BETA1-3 : bond 0.00861 ( 2) link_BETA1-3 : angle 3.17249 ( 6) covalent geometry : bond 0.00291 (10276) covalent geometry : angle 0.74543 (13896) ********************** 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 319 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 1.494 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 54 MET cc_start: 0.7757 (tpp) cc_final: 0.6974 (tpp) REVERT: A 59 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 80 LYS cc_start: 0.8059 (mttt) cc_final: 0.7550 (mttt) REVERT: A 83 GLN cc_start: 0.7243 (mt0) cc_final: 0.6663 (mt0) REVERT: A 88 TYR cc_start: 0.7274 (p90) cc_final: 0.7064 (p90) REVERT: A 165 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7716 (ttt180) REVERT: A 168 VAL cc_start: 0.8398 (t) cc_final: 0.8156 (p) REVERT: A 210 LEU cc_start: 0.8439 (mm) cc_final: 0.8213 (mm) REVERT: A 252 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6931 (mtp-110) REVERT: A 335 LYS cc_start: 0.7390 (tptp) cc_final: 0.7165 (tptp) REVERT: A 350 SER cc_start: 0.7204 (t) cc_final: 0.6948 (p) REVERT: A 357 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7807 (mtmm) REVERT: A 399 LYS cc_start: 0.7119 (mtpp) cc_final: 0.6740 (mtpp) REVERT: A 405 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7328 (tp) REVERT: A 426 ILE cc_start: 0.8102 (mt) cc_final: 0.7455 (tt) REVERT: A 452 SER cc_start: 0.7557 (p) cc_final: 0.6623 (t) REVERT: A 454 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7525 (mmtt) REVERT: A 458 ASP cc_start: 0.7787 (t0) cc_final: 0.7331 (t0) REVERT: A 521 ARG cc_start: 0.7459 (ppt-90) cc_final: 0.6869 (ppt-90) REVERT: A 522 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6120 (t0) REVERT: A 548 GLU cc_start: 0.5061 (mp0) cc_final: 0.4462 (mm-30) REVERT: A 561 GLU cc_start: 0.5627 (tp30) cc_final: 0.4159 (tp30) REVERT: A 586 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6506 (tp) REVERT: A 600 MET cc_start: 0.6242 (tpp) cc_final: 0.5708 (tpp) REVERT: A 618 HIS cc_start: 0.7010 (m-70) cc_final: 0.6628 (m170) REVERT: C 49 TRP cc_start: 0.7378 (m-10) cc_final: 0.7156 (m100) REVERT: B 32 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7483 (mt0) REVERT: B 59 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 66 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6083 (mt-10) REVERT: B 80 LYS cc_start: 0.8339 (mttt) cc_final: 0.7708 (mttt) REVERT: B 98 ARG cc_start: 0.7726 (ttt90) cc_final: 0.7326 (mmm-85) REVERT: B 149 ARG cc_start: 0.7381 (ttt90) cc_final: 0.6873 (ttt-90) REVERT: B 168 VAL cc_start: 0.8223 (t) cc_final: 0.7854 (p) REVERT: B 171 ASP cc_start: 0.7305 (t0) cc_final: 0.7083 (t0) REVERT: B 210 LEU cc_start: 0.8314 (mm) cc_final: 0.7780 (tp) REVERT: B 235 GLN cc_start: 0.7340 (mm110) cc_final: 0.6741 (mm-40) REVERT: B 260 CYS cc_start: 0.6228 (OUTLIER) cc_final: 0.3248 (t) REVERT: B 261 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7051 (mmtt) REVERT: B 263 THR cc_start: 0.8371 (m) cc_final: 0.8165 (p) REVERT: B 278 ASP cc_start: 0.7326 (m-30) cc_final: 0.6924 (m-30) REVERT: B 286 SER cc_start: 0.7272 (m) cc_final: 0.7018 (m) REVERT: B 350 SER cc_start: 0.6910 (t) cc_final: 0.6649 (p) REVERT: B 364 SER cc_start: 0.8871 (p) cc_final: 0.8562 (m) REVERT: B 382 THR cc_start: 0.3790 (OUTLIER) cc_final: 0.3576 (m) REVERT: B 399 LYS cc_start: 0.7064 (mtpp) cc_final: 0.6626 (mtpp) REVERT: B 451 ARG cc_start: 0.7352 (ptp-110) cc_final: 0.6968 (mtm-85) REVERT: B 454 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7606 (mmtt) REVERT: B 458 ASP cc_start: 0.7758 (t0) cc_final: 0.7134 (t0) REVERT: B 487 LYS cc_start: 0.7851 (pttp) cc_final: 0.7460 (pttp) REVERT: B 502 THR cc_start: 0.8330 (p) cc_final: 0.8103 (t) REVERT: B 522 ASP cc_start: 0.6601 (m-30) cc_final: 0.6108 (m-30) REVERT: B 534 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6561 (mt-10) REVERT: B 561 GLU cc_start: 0.6315 (tp30) cc_final: 0.6046 (tp30) REVERT: B 618 HIS cc_start: 0.6941 (m-70) cc_final: 0.6631 (m-70) outliers start: 17 outliers final: 11 residues processed: 309 average time/residue: 0.2786 time to fit residues: 113.3419 Evaluate side-chains 317 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 300 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 536 VAL 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 D residue 50 TRP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 100 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 504 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 235 GLN B 486 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134048 restraints weight = 15173.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138424 restraints weight = 7785.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141330 restraints weight = 4777.042| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10340 Z= 0.152 Angle : 0.782 10.758 14036 Z= 0.379 Chirality : 0.050 0.330 1550 Planarity : 0.004 0.055 1814 Dihedral : 7.115 55.048 1620 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 2.23 % Allowed : 20.89 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1272 helix: -1.23 (0.85), residues: 40 sheet: -1.74 (0.71), residues: 54 loop : -1.05 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 49 HIS 0.004 0.001 HIS A 370 PHE 0.034 0.002 PHE B 180 TYR 0.021 0.002 TYR D 22 ARG 0.007 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 6) link_NAG-ASN : angle 4.69452 ( 18) link_BETA1-4 : bond 0.00805 ( 2) link_BETA1-4 : angle 2.01267 ( 6) link_ALPHA1-3 : bond 0.02435 ( 2) link_ALPHA1-3 : angle 3.92494 ( 6) hydrogen bonds : bond 0.03604 ( 138) hydrogen bonds : angle 6.19527 ( 252) SS BOND : bond 0.00415 ( 52) SS BOND : angle 1.38247 ( 104) link_BETA1-3 : bond 0.00687 ( 2) link_BETA1-3 : angle 3.25326 ( 6) covalent geometry : bond 0.00342 (10276) covalent geometry : angle 0.74973 (13896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.28 seconds wall clock time: 68 minutes 30.06 seconds (4110.06 seconds total)