Starting phenix.real_space_refine on Tue Nov 19 02:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_34746.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_34746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_34746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_34746.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgs_34746/11_2024/8hgs_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): 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.92, per 1000 atoms: 0.69 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: 2.57 Conformation dependent library (CDL) restraints added in 1.5 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: 1.46 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: 3.51 Time building geometry restraints manager: 2.97 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.390 Find NCS groups from input model: 0.310 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- 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 10276 Z= 0.262 Angle : 0.748 9.519 13896 Z= 0.396 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 *********************** 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 : 1.028 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: 0.2951 time to fit residues: 125.1360 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 : 1.178 ------------------------------------------------------------------------------- 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: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 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 10276 Z= 0.290 Angle : 0.729 13.198 13896 Z= 0.366 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 *********************** 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 : 1.080 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: 0.8017 (mm110) cc_final: 0.7396 (mp10) REVERT: A 37 LYS cc_start: 0.8095 (mttt) cc_final: 0.7809 (mttp) REVERT: A 46 ASP cc_start: 0.7435 (m-30) cc_final: 0.6863 (m-30) REVERT: A 54 MET cc_start: 0.7322 (tpp) cc_final: 0.7069 (tpp) REVERT: A 58 CYS cc_start: 0.5214 (t) cc_final: 0.4949 (t) REVERT: A 59 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 78 PHE cc_start: 0.8324 (p90) cc_final: 0.8048 (p90) REVERT: A 80 LYS cc_start: 0.8081 (mttt) cc_final: 0.7638 (mtmt) REVERT: A 105 GLN cc_start: 0.7965 (mt0) cc_final: 0.7481 (mt0) REVERT: A 108 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6750 (mmm-85) REVERT: A 112 TYR cc_start: 0.7103 (m-80) cc_final: 0.6862 (m-80) REVERT: A 125 TYR cc_start: 0.7453 (p90) cc_final: 0.7066 (p90) REVERT: A 139 ASN cc_start: 0.7996 (m110) cc_final: 0.7502 (m-40) REVERT: A 143 ILE cc_start: 0.8039 (mt) cc_final: 0.7828 (mp) REVERT: A 149 ARG cc_start: 0.6859 (ttt90) cc_final: 0.6649 (ttt-90) REVERT: A 246 SER cc_start: 0.8238 (p) cc_final: 0.8036 (m) REVERT: A 252 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.7120 (ttt-90) REVERT: A 253 LYS cc_start: 0.8094 (mttp) cc_final: 0.7094 (mttp) REVERT: A 255 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6701 (ttt-90) REVERT: A 268 MET cc_start: 0.7029 (mmt) cc_final: 0.6703 (mmt) REVERT: A 340 ILE cc_start: 0.7879 (mp) cc_final: 0.7503 (mt) REVERT: A 350 SER cc_start: 0.6761 (t) cc_final: 0.6431 (p) REVERT: A 399 LYS cc_start: 0.6865 (mtpp) cc_final: 0.6446 (mtpp) REVERT: A 400 GLU cc_start: 0.7078 (tt0) cc_final: 0.6867 (tt0) REVERT: A 405 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6765 (tp) REVERT: A 422 ASN cc_start: 0.7796 (m-40) cc_final: 0.7339 (m-40) REVERT: A 452 SER cc_start: 0.6974 (p) cc_final: 0.6772 (t) REVERT: A 458 ASP cc_start: 0.7624 (t0) cc_final: 0.7082 (t0) REVERT: A 548 GLU cc_start: 0.4980 (mp0) cc_final: 0.4446 (mp0) REVERT: A 559 HIS cc_start: 0.6722 (t-90) cc_final: 0.6394 (t-90) REVERT: A 574 ARG cc_start: 0.7322 (ptp90) cc_final: 0.6990 (mpp-170) REVERT: A 618 HIS cc_start: 0.6635 (m-70) cc_final: 0.6226 (m-70) REVERT: B 59 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6760 (mt-10) REVERT: B 80 LYS cc_start: 0.8365 (mttt) cc_final: 0.7782 (mttt) REVERT: B 88 TYR cc_start: 0.7681 (p90) cc_final: 0.7353 (p90) REVERT: B 149 ARG cc_start: 0.6995 (ttt90) cc_final: 0.6718 (ttt90) REVERT: B 168 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7637 (p) REVERT: B 171 ASP cc_start: 0.7089 (t0) cc_final: 0.6728 (t0) REVERT: B 253 LYS cc_start: 0.8091 (mttp) cc_final: 0.7798 (mttp) REVERT: B 278 ASP cc_start: 0.7105 (m-30) cc_final: 0.6561 (m-30) REVERT: B 309 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6220 (mmt90) REVERT: B 321 ASP cc_start: 0.6098 (m-30) cc_final: 0.5810 (m-30) REVERT: B 325 LYS cc_start: 0.8105 (mmtp) cc_final: 0.7885 (mmtp) REVERT: B 345 PHE cc_start: 0.7293 (m-10) cc_final: 0.6892 (m-10) REVERT: B 360 LYS cc_start: 0.7962 (tppp) cc_final: 0.7709 (tppp) REVERT: B 364 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8394 (m) REVERT: B 369 LEU cc_start: 0.7991 (mt) cc_final: 0.7603 (mt) REVERT: B 399 LYS cc_start: 0.6821 (mtpp) cc_final: 0.6220 (mtpp) REVERT: B 400 GLU cc_start: 0.7273 (tt0) cc_final: 0.6994 (tt0) REVERT: B 452 SER cc_start: 0.6731 (p) cc_final: 0.5754 (p) REVERT: B 454 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7484 (mmtt) REVERT: B 458 ASP cc_start: 0.7673 (t0) cc_final: 0.7013 (t0) REVERT: B 460 ASP cc_start: 0.6337 (m-30) cc_final: 0.5726 (m-30) REVERT: B 475 ILE cc_start: 0.6714 (mm) cc_final: 0.6482 (mp) REVERT: B 487 LYS cc_start: 0.7235 (pttp) cc_final: 0.6601 (pttp) REVERT: B 521 ARG cc_start: 0.6952 (ppt-90) cc_final: 0.6593 (ppt-90) REVERT: B 618 HIS cc_start: 0.6768 (m-70) cc_final: 0.6425 (m90) outliers start: 22 outliers final: 10 residues processed: 309 average time/residue: 0.2892 time to fit residues: 115.7509 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 : 1.086 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10276 Z= 0.256 Angle : 0.717 9.677 13896 Z= 0.357 Chirality : 0.051 0.320 1550 Planarity : 0.004 0.067 1814 Dihedral : 10.206 68.446 1620 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.14 % Allowed : 10.45 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (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: -2.16 (0.22), residues: 1272 helix: -0.46 (0.92), residues: 42 sheet: -2.04 (0.64), residues: 44 loop : -1.63 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS B 559 PHE 0.015 0.002 PHE B 180 TYR 0.017 0.002 TYR D 37 ARG 0.007 0.001 ARG A 72 *********************** 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 310 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 1.055 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: 0.8041 (mm110) cc_final: 0.7804 (mp10) REVERT: A 37 LYS cc_start: 0.8012 (mttt) cc_final: 0.7564 (mttm) REVERT: A 46 ASP cc_start: 0.7471 (m-30) cc_final: 0.6908 (m-30) REVERT: A 58 CYS cc_start: 0.5350 (t) cc_final: 0.5086 (t) REVERT: A 59 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7217 (mt-10) REVERT: A 64 ASN cc_start: 0.8105 (m-40) cc_final: 0.7464 (m-40) REVERT: A 78 PHE cc_start: 0.8349 (p90) cc_final: 0.8031 (p90) REVERT: A 80 LYS cc_start: 0.8165 (mttt) cc_final: 0.7624 (mtmt) REVERT: A 105 GLN cc_start: 0.8023 (mt0) cc_final: 0.7756 (mt0) REVERT: A 125 TYR cc_start: 0.7476 (p90) cc_final: 0.7105 (p90) REVERT: A 139 ASN cc_start: 0.8045 (m110) cc_final: 0.7524 (m-40) REVERT: A 149 ARG cc_start: 0.6928 (ttt90) cc_final: 0.6477 (ttp80) REVERT: A 222 ARG cc_start: 0.5918 (mtp85) cc_final: 0.5376 (mtt90) REVERT: A 252 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6994 (ttp80) REVERT: A 254 PHE cc_start: 0.7529 (m-10) cc_final: 0.7326 (m-80) REVERT: A 263 THR cc_start: 0.8413 (p) cc_final: 0.8210 (p) REVERT: A 271 ASN cc_start: 0.7864 (t0) cc_final: 0.7566 (t0) REVERT: A 335 LYS cc_start: 0.7594 (tptp) cc_final: 0.7232 (tptp) REVERT: A 350 SER cc_start: 0.6865 (t) cc_final: 0.6440 (p) REVERT: A 399 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6535 (mtpp) REVERT: A 400 GLU cc_start: 0.7201 (tt0) cc_final: 0.6958 (tt0) REVERT: A 405 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6591 (tp) REVERT: A 426 ILE cc_start: 0.7548 (mt) cc_final: 0.6966 (tt) REVERT: A 436 PHE cc_start: 0.7140 (m-80) cc_final: 0.6644 (m-80) REVERT: A 452 SER cc_start: 0.7154 (p) cc_final: 0.6900 (t) REVERT: A 458 ASP cc_start: 0.7819 (t0) cc_final: 0.7234 (t0) REVERT: A 489 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7750 (mtmt) REVERT: A 548 GLU cc_start: 0.4878 (mp0) cc_final: 0.4443 (mp0) REVERT: A 561 GLU cc_start: 0.6010 (tp30) cc_final: 0.3157 (mm-30) REVERT: A 574 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7420 (mpp-170) REVERT: A 618 HIS cc_start: 0.6866 (m-70) cc_final: 0.6283 (m170) REVERT: B 59 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 66 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6368 (mt-10) REVERT: B 80 LYS cc_start: 0.8390 (mttt) cc_final: 0.7790 (mttt) REVERT: B 88 TYR cc_start: 0.7596 (p90) cc_final: 0.7254 (p90) REVERT: B 149 ARG cc_start: 0.7043 (ttt90) cc_final: 0.6610 (ttt-90) REVERT: B 171 ASP cc_start: 0.7206 (t0) cc_final: 0.6763 (t0) REVERT: B 235 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6996 (mm110) REVERT: B 253 LYS cc_start: 0.7899 (mttp) cc_final: 0.7668 (mttp) REVERT: B 260 CYS cc_start: 0.5734 (OUTLIER) cc_final: 0.4600 (m) REVERT: B 271 ASN cc_start: 0.7841 (t0) cc_final: 0.7300 (m-40) REVERT: B 278 ASP cc_start: 0.7145 (m-30) cc_final: 0.6084 (m-30) REVERT: B 309 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6692 (mtt-85) REVERT: B 325 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7946 (mmtp) REVERT: B 345 PHE cc_start: 0.7422 (m-10) cc_final: 0.7112 (m-10) REVERT: B 361 ASN cc_start: 0.7079 (m-40) cc_final: 0.6828 (t0) REVERT: B 364 SER cc_start: 0.8744 (p) cc_final: 0.8412 (m) REVERT: B 369 LEU cc_start: 0.8062 (mt) cc_final: 0.7710 (mt) REVERT: B 382 THR cc_start: 0.1812 (OUTLIER) cc_final: 0.1586 (m) REVERT: B 391 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7101 (mt-10) REVERT: B 399 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6360 (mtpp) REVERT: B 451 ARG cc_start: 0.7245 (ptp90) cc_final: 0.5929 (ptp90) REVERT: B 454 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7503 (mmtt) REVERT: B 458 ASP cc_start: 0.7732 (t0) cc_final: 0.7058 (t0) REVERT: B 460 ASP cc_start: 0.6338 (m-30) cc_final: 0.6011 (m-30) REVERT: B 475 ILE cc_start: 0.7068 (mm) cc_final: 0.6843 (mp) REVERT: B 487 LYS cc_start: 0.7488 (pttp) cc_final: 0.7074 (pttp) REVERT: B 489 LYS cc_start: 0.7495 (ttmt) cc_final: 0.7269 (ttmt) REVERT: B 521 ARG cc_start: 0.7073 (ppt-90) cc_final: 0.6745 (ppt-90) REVERT: B 559 HIS cc_start: 0.6252 (t-90) cc_final: 0.5941 (t-90) REVERT: B 581 GLN cc_start: 0.7904 (tt0) cc_final: 0.7703 (tt0) REVERT: B 618 HIS cc_start: 0.7063 (m-70) cc_final: 0.6580 (m90) outliers start: 24 outliers final: 10 residues processed: 296 average time/residue: 0.2947 time to fit residues: 113.3170 Evaluate side-chains 280 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 260 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 388 ASP 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 113 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 54 optimal weight: 0.0570 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 298 ASN A 540 ASN B 32 GLN B 71 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10276 Z= 0.268 Angle : 0.738 15.355 13896 Z= 0.360 Chirality : 0.051 0.319 1550 Planarity : 0.004 0.043 1814 Dihedral : 8.963 62.965 1620 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.23 % Allowed : 13.04 % Favored : 84.73 % 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: -2.05 (0.22), residues: 1272 helix: -0.50 (0.92), residues: 40 sheet: -2.13 (0.63), residues: 44 loop : -1.53 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.005 0.001 HIS A 418 PHE 0.028 0.002 PHE B 404 TYR 0.017 0.001 TYR D 37 ARG 0.007 0.001 ARG B 427 *********************** 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 299 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.116 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: 0.8041 (mm110) cc_final: 0.7401 (mt0) REVERT: A 46 ASP cc_start: 0.7364 (m-30) cc_final: 0.6855 (m-30) REVERT: A 58 CYS cc_start: 0.5366 (t) cc_final: 0.5032 (t) REVERT: A 59 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 64 ASN cc_start: 0.8067 (m-40) cc_final: 0.7525 (m-40) REVERT: A 78 PHE cc_start: 0.8369 (p90) cc_final: 0.8046 (p90) REVERT: A 80 LYS cc_start: 0.8242 (mttt) cc_final: 0.7659 (mtmt) REVERT: A 105 GLN cc_start: 0.8021 (mt0) cc_final: 0.7805 (mt0) REVERT: A 111 MET cc_start: 0.7453 (ptm) cc_final: 0.7157 (ptm) REVERT: A 125 TYR cc_start: 0.7587 (p90) cc_final: 0.7334 (p90) REVERT: A 137 MET cc_start: 0.7491 (mtp) cc_final: 0.7186 (mtm) REVERT: A 149 ARG cc_start: 0.7031 (ttt90) cc_final: 0.6451 (ttp80) REVERT: A 210 LEU cc_start: 0.8348 (mm) cc_final: 0.8009 (mm) REVERT: A 222 ARG cc_start: 0.6090 (mtp85) cc_final: 0.5545 (mtt90) REVERT: A 235 GLN cc_start: 0.7187 (mm110) cc_final: 0.6815 (mm-40) REVERT: A 252 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6878 (ttp80) REVERT: A 253 LYS cc_start: 0.8100 (mttp) cc_final: 0.6955 (mttp) REVERT: A 335 LYS cc_start: 0.7517 (tptp) cc_final: 0.7191 (tptp) REVERT: A 350 SER cc_start: 0.6871 (t) cc_final: 0.6535 (p) REVERT: A 357 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7746 (mtmm) REVERT: A 399 LYS cc_start: 0.7073 (mtpp) cc_final: 0.6576 (mtpp) REVERT: A 405 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6534 (tp) REVERT: A 426 ILE cc_start: 0.7555 (mt) cc_final: 0.6971 (tt) REVERT: A 452 SER cc_start: 0.7194 (p) cc_final: 0.6861 (t) REVERT: A 458 ASP cc_start: 0.7772 (t0) cc_final: 0.7155 (t0) REVERT: A 460 ASP cc_start: 0.6349 (m-30) cc_final: 0.5965 (m-30) REVERT: A 521 ARG cc_start: 0.7357 (ppt-90) cc_final: 0.6779 (ppt-90) REVERT: A 548 GLU cc_start: 0.4801 (mp0) cc_final: 0.4325 (mp0) REVERT: A 559 HIS cc_start: 0.6670 (t-90) cc_final: 0.6460 (t-90) REVERT: A 618 HIS cc_start: 0.6999 (m-70) cc_final: 0.6415 (m170) REVERT: B 32 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7511 (mt0) REVERT: B 59 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 66 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6312 (mt-10) REVERT: B 80 LYS cc_start: 0.8395 (mttt) cc_final: 0.7757 (mttt) REVERT: B 88 TYR cc_start: 0.7572 (p90) cc_final: 0.7274 (p90) REVERT: B 112 TYR cc_start: 0.7788 (m-80) cc_final: 0.6416 (m-80) REVERT: B 149 ARG cc_start: 0.7162 (ttt90) cc_final: 0.6719 (ttt-90) REVERT: B 168 VAL cc_start: 0.8118 (t) cc_final: 0.7726 (p) REVERT: B 171 ASP cc_start: 0.7279 (t0) cc_final: 0.6865 (t0) REVERT: B 235 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6962 (mm-40) REVERT: B 260 CYS cc_start: 0.5875 (OUTLIER) cc_final: 0.4785 (m) REVERT: B 271 ASN cc_start: 0.7900 (t0) cc_final: 0.7245 (m-40) REVERT: B 278 ASP cc_start: 0.7197 (m-30) cc_final: 0.5976 (m-30) REVERT: B 286 SER cc_start: 0.6851 (m) cc_final: 0.6441 (m) REVERT: B 325 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7999 (mmtp) REVERT: B 357 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7748 (ptmm) REVERT: B 361 ASN cc_start: 0.7183 (m-40) cc_final: 0.6908 (t0) REVERT: B 364 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8385 (m) REVERT: B 369 LEU cc_start: 0.8064 (mt) cc_final: 0.7744 (mt) REVERT: B 388 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6845 (p0) REVERT: B 399 LYS cc_start: 0.6899 (mtpp) cc_final: 0.6292 (mtpp) REVERT: B 415 THR cc_start: 0.7381 (p) cc_final: 0.7051 (t) REVERT: B 454 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7500 (mmtt) REVERT: B 458 ASP cc_start: 0.7797 (t0) cc_final: 0.7242 (t0) REVERT: B 460 ASP cc_start: 0.6411 (m-30) cc_final: 0.6114 (m-30) REVERT: B 475 ILE cc_start: 0.7160 (mm) cc_final: 0.6927 (mp) REVERT: B 487 LYS cc_start: 0.7579 (pttp) cc_final: 0.7035 (pttp) REVERT: B 502 THR cc_start: 0.8171 (p) cc_final: 0.7937 (t) REVERT: B 521 ARG cc_start: 0.7261 (ppt-90) cc_final: 0.6407 (ppt-90) REVERT: B 559 HIS cc_start: 0.6774 (t-90) cc_final: 0.6425 (t-90) REVERT: B 581 GLN cc_start: 0.7676 (tt0) cc_final: 0.7393 (tt0) REVERT: B 618 HIS cc_start: 0.7258 (m-70) cc_final: 0.6697 (m90) outliers start: 25 outliers final: 10 residues processed: 285 average time/residue: 0.2873 time to fit residues: 107.9301 Evaluate side-chains 281 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 269 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain 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 388 ASP Chi-restraints excluded: chain B residue 462 ILE 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 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 466 ASN A 504 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10276 Z= 0.284 Angle : 0.719 9.738 13896 Z= 0.358 Chirality : 0.051 0.326 1550 Planarity : 0.005 0.073 1814 Dihedral : 8.173 56.875 1620 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.14 % Allowed : 13.66 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (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: -1.91 (0.23), residues: 1272 helix: -1.03 (0.83), residues: 42 sheet: -1.86 (0.66), residues: 54 loop : -1.40 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 49 HIS 0.005 0.001 HIS D 16 PHE 0.031 0.002 PHE B 404 TYR 0.018 0.002 TYR D 37 ARG 0.008 0.001 ARG B 533 *********************** 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 310 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7294 (mttp) cc_final: 0.7052 (mttp) REVERT: A 32 GLN cc_start: 0.8114 (mm110) cc_final: 0.7420 (mt0) REVERT: A 46 ASP cc_start: 0.7404 (m-30) cc_final: 0.6908 (m-30) REVERT: A 58 CYS cc_start: 0.5244 (t) cc_final: 0.4872 (t) REVERT: A 59 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 64 ASN cc_start: 0.8186 (m-40) cc_final: 0.7508 (m-40) REVERT: A 78 PHE cc_start: 0.8448 (p90) cc_final: 0.8087 (p90) REVERT: A 80 LYS cc_start: 0.8447 (mttt) cc_final: 0.7801 (mtmt) REVERT: A 105 GLN cc_start: 0.8080 (mt0) cc_final: 0.7864 (mt0) REVERT: A 111 MET cc_start: 0.7350 (ptm) cc_final: 0.7055 (ptm) REVERT: A 125 TYR cc_start: 0.7695 (p90) cc_final: 0.7450 (p90) REVERT: A 137 MET cc_start: 0.7435 (mtp) cc_final: 0.7128 (mtm) REVERT: A 149 ARG cc_start: 0.7173 (ttt90) cc_final: 0.6553 (ttp80) REVERT: A 210 LEU cc_start: 0.8388 (mm) cc_final: 0.8120 (mm) REVERT: A 222 ARG cc_start: 0.6334 (mtp85) cc_final: 0.5879 (mtt90) REVERT: A 252 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.6996 (ttp80) REVERT: A 253 LYS cc_start: 0.8244 (mttp) cc_final: 0.7469 (mttp) REVERT: A 335 LYS cc_start: 0.7528 (tptp) cc_final: 0.7232 (tptp) REVERT: A 350 SER cc_start: 0.6933 (t) cc_final: 0.6632 (p) REVERT: A 357 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7826 (mtmm) REVERT: A 382 THR cc_start: 0.1427 (OUTLIER) cc_final: 0.1227 (m) REVERT: A 399 LYS cc_start: 0.7024 (mtpp) cc_final: 0.6577 (mtpp) REVERT: A 405 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6613 (tp) REVERT: A 415 THR cc_start: 0.7463 (p) cc_final: 0.7136 (t) REVERT: A 426 ILE cc_start: 0.7564 (mt) cc_final: 0.6977 (tt) REVERT: A 452 SER cc_start: 0.7253 (p) cc_final: 0.5956 (t) REVERT: A 454 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7474 (mmtt) REVERT: A 458 ASP cc_start: 0.7801 (t0) cc_final: 0.7235 (t0) REVERT: A 460 ASP cc_start: 0.6480 (m-30) cc_final: 0.6143 (m-30) REVERT: A 521 ARG cc_start: 0.7432 (ppt-90) cc_final: 0.6874 (ppt-90) REVERT: A 618 HIS cc_start: 0.7298 (m-70) cc_final: 0.6617 (m-70) REVERT: C 37 TYR cc_start: 0.7992 (m-10) cc_final: 0.7780 (m-10) REVERT: B 32 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7488 (mt0) REVERT: B 59 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7147 (mt-10) REVERT: B 66 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6282 (mt-10) REVERT: B 80 LYS cc_start: 0.8427 (mttt) cc_final: 0.7798 (mttt) REVERT: B 88 TYR cc_start: 0.7525 (p90) cc_final: 0.7190 (p90) REVERT: B 149 ARG cc_start: 0.7195 (ttt90) cc_final: 0.6724 (ttt-90) REVERT: B 168 VAL cc_start: 0.8126 (t) cc_final: 0.7826 (p) REVERT: B 171 ASP cc_start: 0.7372 (t0) cc_final: 0.6771 (t0) REVERT: B 172 PHE cc_start: 0.8100 (m-10) cc_final: 0.7440 (m-10) REVERT: B 235 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6298 (mm-40) REVERT: B 252 ARG cc_start: 0.7173 (ttt-90) cc_final: 0.6654 (ttp80) REVERT: B 260 CYS cc_start: 0.6136 (OUTLIER) cc_final: 0.4697 (m) REVERT: B 261 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7173 (mmtt) REVERT: B 271 ASN cc_start: 0.7909 (t0) cc_final: 0.7436 (m-40) REVERT: B 286 SER cc_start: 0.6916 (m) cc_final: 0.6510 (m) REVERT: B 325 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7843 (mmtm) REVERT: B 357 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7777 (pttp) REVERT: B 364 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 369 LEU cc_start: 0.8091 (mt) cc_final: 0.7799 (mt) REVERT: B 399 LYS cc_start: 0.6974 (mtpp) cc_final: 0.6432 (mtpp) REVERT: B 415 THR cc_start: 0.7659 (p) cc_final: 0.7174 (t) REVERT: B 454 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7512 (mmtt) REVERT: B 458 ASP cc_start: 0.7806 (t0) cc_final: 0.7533 (t0) REVERT: B 475 ILE cc_start: 0.7286 (mm) cc_final: 0.7065 (mp) REVERT: B 487 LYS cc_start: 0.7706 (pttp) cc_final: 0.7474 (pttp) REVERT: B 502 THR cc_start: 0.8266 (p) cc_final: 0.8062 (t) REVERT: B 521 ARG cc_start: 0.7281 (ppt-90) cc_final: 0.7079 (tmm-80) REVERT: B 534 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6804 (mp0) REVERT: B 559 HIS cc_start: 0.6984 (t-90) cc_final: 0.6779 (t-90) REVERT: B 618 HIS cc_start: 0.7381 (m-70) cc_final: 0.6942 (m-70) outliers start: 24 outliers final: 12 residues processed: 295 average time/residue: 0.2817 time to fit residues: 109.6124 Evaluate side-chains 297 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 281 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 134 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 462 ILE 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 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 493 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10276 Z= 0.371 Angle : 0.781 9.834 13896 Z= 0.394 Chirality : 0.053 0.326 1550 Planarity : 0.004 0.042 1814 Dihedral : 8.073 55.671 1620 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.41 % Allowed : 15.27 % 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: -1.82 (0.23), residues: 1272 helix: -1.36 (0.79), residues: 42 sheet: -1.89 (0.69), residues: 54 loop : -1.31 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 49 HIS 0.007 0.001 HIS A 559 PHE 0.032 0.003 PHE B 404 TYR 0.015 0.002 TYR D 37 ARG 0.008 0.001 ARG A 414 *********************** 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 328 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7328 (mttp) cc_final: 0.7089 (mttp) REVERT: A 32 GLN cc_start: 0.8167 (mm110) cc_final: 0.7414 (mt0) REVERT: A 54 MET cc_start: 0.7696 (tpp) cc_final: 0.7326 (tpp) REVERT: A 58 CYS cc_start: 0.5254 (t) cc_final: 0.4836 (t) REVERT: A 59 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7246 (mt-10) REVERT: A 78 PHE cc_start: 0.8408 (p90) cc_final: 0.8104 (p90) REVERT: A 80 LYS cc_start: 0.8509 (mttt) cc_final: 0.7833 (mttt) REVERT: A 111 MET cc_start: 0.7382 (ptm) cc_final: 0.7171 (ptm) REVERT: A 137 MET cc_start: 0.7435 (mtp) cc_final: 0.7126 (mtm) REVERT: A 149 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6758 (ttt-90) REVERT: A 171 ASP cc_start: 0.6900 (t0) cc_final: 0.6385 (t0) REVERT: A 172 PHE cc_start: 0.7986 (m-10) cc_final: 0.7334 (m-10) REVERT: A 210 LEU cc_start: 0.8521 (mm) cc_final: 0.8286 (mm) REVERT: A 222 ARG cc_start: 0.6571 (mtp85) cc_final: 0.6125 (mtt90) REVERT: A 253 LYS cc_start: 0.8326 (mttp) cc_final: 0.7919 (mttp) REVERT: A 256 ASP cc_start: 0.6709 (m-30) cc_final: 0.6496 (m-30) REVERT: A 335 LYS cc_start: 0.7529 (tptp) cc_final: 0.7223 (tptp) REVERT: A 350 SER cc_start: 0.7044 (t) cc_final: 0.6784 (p) REVERT: A 357 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7768 (mtmm) REVERT: A 399 LYS cc_start: 0.7130 (mtpp) cc_final: 0.6660 (mtpp) REVERT: A 405 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6594 (tp) REVERT: A 415 THR cc_start: 0.7701 (p) cc_final: 0.7333 (t) REVERT: A 426 ILE cc_start: 0.7659 (mt) cc_final: 0.7089 (tt) REVERT: A 427 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7838 (mmt90) REVERT: A 451 ARG cc_start: 0.7454 (ptp90) cc_final: 0.7014 (ptp90) REVERT: A 452 SER cc_start: 0.7343 (p) cc_final: 0.6282 (t) REVERT: A 454 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7428 (mmtt) REVERT: A 458 ASP cc_start: 0.7803 (t0) cc_final: 0.7316 (t0) REVERT: A 521 ARG cc_start: 0.7543 (ppt-90) cc_final: 0.7243 (ptt-90) REVERT: A 548 GLU cc_start: 0.5752 (mp0) cc_final: 0.5503 (mp0) REVERT: A 586 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 618 HIS cc_start: 0.7399 (m-70) cc_final: 0.6824 (m-70) REVERT: B 32 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: B 54 MET cc_start: 0.7882 (tpp) cc_final: 0.7478 (tpp) REVERT: B 59 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 66 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6401 (mt-10) REVERT: B 80 LYS cc_start: 0.8518 (mttt) cc_final: 0.7880 (mttt) REVERT: B 88 TYR cc_start: 0.7501 (p90) cc_final: 0.7107 (p90) REVERT: B 111 MET cc_start: 0.7084 (ptm) cc_final: 0.6592 (ptm) REVERT: B 139 ASN cc_start: 0.7928 (m110) cc_final: 0.7700 (m-40) REVERT: B 149 ARG cc_start: 0.7240 (ttt90) cc_final: 0.6718 (ttt-90) REVERT: B 168 VAL cc_start: 0.8212 (t) cc_final: 0.7912 (p) REVERT: B 171 ASP cc_start: 0.7392 (t0) cc_final: 0.6773 (t0) REVERT: B 172 PHE cc_start: 0.8091 (m-10) cc_final: 0.7504 (m-10) REVERT: B 210 LEU cc_start: 0.8414 (mm) cc_final: 0.7920 (tp) REVERT: B 235 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6494 (mm-40) REVERT: B 252 ARG cc_start: 0.7184 (ttt-90) cc_final: 0.6748 (ttp80) REVERT: B 260 CYS cc_start: 0.6270 (OUTLIER) cc_final: 0.4719 (m) REVERT: B 261 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7253 (mmtt) REVERT: B 263 THR cc_start: 0.8549 (m) cc_final: 0.8173 (p) REVERT: B 271 ASN cc_start: 0.7890 (t0) cc_final: 0.7398 (m-40) REVERT: B 286 SER cc_start: 0.7001 (m) cc_final: 0.6628 (m) REVERT: B 325 LYS cc_start: 0.8250 (mmtp) cc_final: 0.7984 (mmtm) REVERT: B 340 ILE cc_start: 0.7913 (mm) cc_final: 0.7702 (mm) REVERT: B 357 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7954 (pttp) REVERT: B 364 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8406 (m) REVERT: B 369 LEU cc_start: 0.8065 (mt) cc_final: 0.7789 (mt) REVERT: B 396 LYS cc_start: 0.7717 (mttt) cc_final: 0.7227 (mttm) REVERT: B 399 LYS cc_start: 0.7014 (mtpp) cc_final: 0.6492 (mtpp) REVERT: B 415 THR cc_start: 0.7737 (p) cc_final: 0.7222 (t) REVERT: B 454 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7519 (mmtt) REVERT: B 458 ASP cc_start: 0.7815 (t0) cc_final: 0.7278 (t0) REVERT: B 475 ILE cc_start: 0.7515 (mm) cc_final: 0.7309 (tp) REVERT: B 487 LYS cc_start: 0.7936 (pttp) cc_final: 0.7558 (pttp) REVERT: B 553 SER cc_start: 0.8115 (m) cc_final: 0.7893 (t) REVERT: B 561 GLU cc_start: 0.6923 (tp30) cc_final: 0.6422 (tp30) REVERT: B 565 GLN cc_start: 0.6815 (mp10) cc_final: 0.6493 (mp10) REVERT: B 618 HIS cc_start: 0.7221 (m-70) cc_final: 0.6748 (m90) outliers start: 27 outliers final: 17 residues processed: 313 average time/residue: 0.3485 time to fit residues: 141.3081 Evaluate side-chains 309 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 130 THR 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 274 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 395 LEU 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 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 89 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10276 Z= 0.212 Angle : 0.737 10.166 13896 Z= 0.363 Chirality : 0.050 0.342 1550 Planarity : 0.004 0.039 1814 Dihedral : 7.545 55.992 1620 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.14 % Allowed : 16.88 % Favored : 80.98 % 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: -1.68 (0.23), residues: 1272 helix: -1.11 (0.84), residues: 40 sheet: -1.98 (0.68), residues: 54 loop : -1.20 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 49 HIS 0.008 0.001 HIS A 418 PHE 0.024 0.002 PHE B 404 TYR 0.016 0.001 TYR C 37 ARG 0.009 0.001 ARG B 533 *********************** 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 322 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 298 time to evaluate : 1.025 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 29 LYS cc_start: 0.7305 (mttp) cc_final: 0.7088 (mttp) REVERT: A 54 MET cc_start: 0.7609 (tpp) cc_final: 0.7212 (tpp) REVERT: A 58 CYS cc_start: 0.5268 (t) cc_final: 0.4850 (t) REVERT: A 59 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 78 PHE cc_start: 0.8328 (p90) cc_final: 0.8046 (p90) REVERT: A 80 LYS cc_start: 0.8492 (mttt) cc_final: 0.7846 (mtmt) REVERT: A 137 MET cc_start: 0.7362 (mtp) cc_final: 0.7071 (mtm) REVERT: A 149 ARG cc_start: 0.7297 (ttt90) cc_final: 0.6732 (ttt-90) REVERT: A 171 ASP cc_start: 0.6836 (t0) cc_final: 0.6337 (t0) REVERT: A 172 PHE cc_start: 0.7892 (m-10) cc_final: 0.7250 (m-10) REVERT: A 210 LEU cc_start: 0.8441 (mm) cc_final: 0.8194 (mm) REVERT: A 222 ARG cc_start: 0.6617 (mtp85) cc_final: 0.6216 (mtt90) REVERT: A 253 LYS cc_start: 0.8317 (mttp) cc_final: 0.8051 (mttp) REVERT: A 335 LYS cc_start: 0.7535 (tptp) cc_final: 0.7258 (tptp) REVERT: A 340 ILE cc_start: 0.8193 (mm) cc_final: 0.7747 (mt) REVERT: A 357 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7792 (mtmm) REVERT: A 361 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6823 (t0) REVERT: A 399 LYS cc_start: 0.7061 (mtpp) cc_final: 0.6564 (mtpp) REVERT: A 405 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6890 (tp) REVERT: A 415 THR cc_start: 0.7535 (p) cc_final: 0.7075 (t) REVERT: A 426 ILE cc_start: 0.7658 (mt) cc_final: 0.7026 (tt) REVERT: A 427 ARG cc_start: 0.8049 (mmt90) cc_final: 0.7358 (mmt90) REVERT: A 451 ARG cc_start: 0.7368 (ptp90) cc_final: 0.6900 (ptp90) REVERT: A 452 SER cc_start: 0.7347 (p) cc_final: 0.6765 (t) REVERT: A 454 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7467 (mmtt) REVERT: A 458 ASP cc_start: 0.7755 (t0) cc_final: 0.7231 (t0) REVERT: A 521 ARG cc_start: 0.7592 (ppt-90) cc_final: 0.7254 (ptt-90) REVERT: A 531 ARG cc_start: 0.6969 (ttm170) cc_final: 0.5453 (ttm170) REVERT: A 548 GLU cc_start: 0.5281 (mp0) cc_final: 0.4940 (mp0) REVERT: A 586 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6719 (tp) REVERT: A 618 HIS cc_start: 0.7289 (m-70) cc_final: 0.6708 (m-70) REVERT: B 32 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: B 54 MET cc_start: 0.7918 (tpp) cc_final: 0.7435 (tpp) REVERT: B 59 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 66 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6246 (mt-10) REVERT: B 80 LYS cc_start: 0.8492 (mttt) cc_final: 0.7847 (mttt) REVERT: B 88 TYR cc_start: 0.7572 (p90) cc_final: 0.7190 (p90) REVERT: B 111 MET cc_start: 0.6981 (ptm) cc_final: 0.6547 (ptm) REVERT: B 139 ASN cc_start: 0.7796 (m110) cc_final: 0.7519 (m-40) REVERT: B 149 ARG cc_start: 0.7286 (ttt90) cc_final: 0.6733 (ttt-90) REVERT: B 168 VAL cc_start: 0.8227 (t) cc_final: 0.7883 (p) REVERT: B 171 ASP cc_start: 0.7368 (t0) cc_final: 0.6760 (t0) REVERT: B 172 PHE cc_start: 0.7993 (m-10) cc_final: 0.7422 (m-10) REVERT: B 210 LEU cc_start: 0.8372 (mm) cc_final: 0.7873 (tp) REVERT: B 235 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6787 (mm-40) REVERT: B 252 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6784 (ttp80) REVERT: B 253 LYS cc_start: 0.8202 (tttm) cc_final: 0.7917 (tttm) REVERT: B 260 CYS cc_start: 0.6207 (OUTLIER) cc_final: 0.4367 (m) REVERT: B 261 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7059 (mmtt) REVERT: B 263 THR cc_start: 0.8434 (m) cc_final: 0.8128 (p) REVERT: B 271 ASN cc_start: 0.7937 (t0) cc_final: 0.7232 (m-40) REVERT: B 286 SER cc_start: 0.7061 (m) cc_final: 0.6683 (m) REVERT: B 325 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7964 (mmtm) REVERT: B 396 LYS cc_start: 0.7765 (mttt) cc_final: 0.7295 (mttm) REVERT: B 399 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6444 (mtpp) REVERT: B 404 PHE cc_start: 0.7932 (p90) cc_final: 0.7729 (p90) REVERT: B 415 THR cc_start: 0.7616 (p) cc_final: 0.7076 (t) REVERT: B 454 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7524 (mmtt) REVERT: B 458 ASP cc_start: 0.7743 (t0) cc_final: 0.7216 (t0) REVERT: B 475 ILE cc_start: 0.7492 (mm) cc_final: 0.7276 (mp) REVERT: B 487 LYS cc_start: 0.7823 (pttp) cc_final: 0.7462 (pttp) REVERT: B 534 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: B 553 SER cc_start: 0.8214 (m) cc_final: 0.7995 (t) REVERT: B 561 GLU cc_start: 0.6683 (tp30) cc_final: 0.5958 (tp30) REVERT: B 581 GLN cc_start: 0.7666 (pp30) cc_final: 0.7224 (pp30) REVERT: B 618 HIS cc_start: 0.7198 (m-70) cc_final: 0.6693 (m90) outliers start: 24 outliers final: 11 residues processed: 309 average time/residue: 0.3270 time to fit residues: 130.9768 Evaluate side-chains 312 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 ASN 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 536 VAL Chi-restraints excluded: chain A residue 559 HIS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10276 Z= 0.258 Angle : 0.750 10.370 13896 Z= 0.370 Chirality : 0.051 0.323 1550 Planarity : 0.004 0.058 1814 Dihedral : 7.421 55.842 1620 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 1.96 % Allowed : 18.21 % Favored : 79.82 % 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 (0.23), residues: 1272 helix: -1.17 (0.84), residues: 40 sheet: -1.89 (0.70), residues: 54 loop : -1.14 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 49 HIS 0.005 0.001 HIS B 507 PHE 0.023 0.002 PHE B 404 TYR 0.021 0.002 TYR C 37 ARG 0.014 0.001 ARG B 533 *********************** 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 322 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7321 (mttp) cc_final: 0.7094 (mttp) REVERT: A 54 MET cc_start: 0.7633 (tpp) cc_final: 0.7162 (tpp) REVERT: A 58 CYS cc_start: 0.5270 (t) cc_final: 0.4867 (t) REVERT: A 59 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 78 PHE cc_start: 0.8348 (p90) cc_final: 0.8081 (p90) REVERT: A 80 LYS cc_start: 0.8547 (mttt) cc_final: 0.7879 (mtmt) REVERT: A 83 GLN cc_start: 0.7401 (mt0) cc_final: 0.6544 (mt0) REVERT: A 124 ASN cc_start: 0.8100 (m-40) cc_final: 0.7865 (m-40) REVERT: A 137 MET cc_start: 0.7363 (mtp) cc_final: 0.7094 (mtm) REVERT: A 149 ARG cc_start: 0.7281 (ttt90) cc_final: 0.6783 (ttt90) REVERT: A 171 ASP cc_start: 0.6909 (t0) cc_final: 0.6380 (t0) REVERT: A 172 PHE cc_start: 0.7897 (m-10) cc_final: 0.7277 (m-10) REVERT: A 210 LEU cc_start: 0.8340 (mm) cc_final: 0.8084 (mm) REVERT: A 253 LYS cc_start: 0.8365 (mttp) cc_final: 0.8094 (mttp) REVERT: A 260 CYS cc_start: 0.6777 (OUTLIER) cc_final: 0.5117 (m) REVERT: A 309 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7420 (mtm-85) REVERT: A 335 LYS cc_start: 0.7596 (tptp) cc_final: 0.7332 (tptp) REVERT: A 357 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7783 (mtmm) REVERT: A 399 LYS cc_start: 0.7103 (mtpp) cc_final: 0.6613 (mtpp) REVERT: A 405 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6933 (tp) REVERT: A 415 THR cc_start: 0.7599 (p) cc_final: 0.7108 (t) REVERT: A 426 ILE cc_start: 0.7679 (mt) cc_final: 0.7063 (tt) REVERT: A 451 ARG cc_start: 0.7410 (ptp90) cc_final: 0.7181 (ptp90) REVERT: A 452 SER cc_start: 0.7365 (p) cc_final: 0.6829 (t) REVERT: A 454 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7499 (mmtt) REVERT: A 458 ASP cc_start: 0.7802 (t0) cc_final: 0.7378 (t0) REVERT: A 489 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7673 (mtmt) REVERT: A 522 ASP cc_start: 0.6996 (m-30) cc_final: 0.5986 (t0) REVERT: A 531 ARG cc_start: 0.6934 (ttm170) cc_final: 0.6681 (ttm170) REVERT: A 548 GLU cc_start: 0.5577 (mp0) cc_final: 0.5191 (mp0) REVERT: A 561 GLU cc_start: 0.5614 (tp30) cc_final: 0.4520 (tp30) REVERT: A 586 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6663 (tp) REVERT: A 618 HIS cc_start: 0.7248 (m-70) cc_final: 0.6636 (m170) REVERT: C 15 LEU cc_start: 0.7758 (mm) cc_final: 0.7504 (mp) REVERT: B 54 MET cc_start: 0.7927 (tpp) cc_final: 0.7379 (tpp) REVERT: B 59 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 66 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5982 (mt-10) REVERT: B 80 LYS cc_start: 0.8512 (mttt) cc_final: 0.7873 (mttt) REVERT: B 88 TYR cc_start: 0.7522 (p90) cc_final: 0.7149 (p90) REVERT: B 111 MET cc_start: 0.7013 (ptm) cc_final: 0.6565 (ptm) REVERT: B 139 ASN cc_start: 0.7840 (m110) cc_final: 0.7551 (m-40) REVERT: B 149 ARG cc_start: 0.7242 (ttt90) cc_final: 0.6627 (ttt-90) REVERT: B 168 VAL cc_start: 0.8236 (t) cc_final: 0.7877 (p) REVERT: B 171 ASP cc_start: 0.7481 (t0) cc_final: 0.6938 (t0) REVERT: B 172 PHE cc_start: 0.8007 (m-10) cc_final: 0.7425 (m-10) REVERT: B 210 LEU cc_start: 0.8364 (mm) cc_final: 0.7777 (tp) REVERT: B 213 ILE cc_start: 0.8152 (pt) cc_final: 0.7899 (pt) REVERT: B 235 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6947 (mm-40) REVERT: B 252 ARG cc_start: 0.7091 (ttt-90) cc_final: 0.6779 (ttp80) REVERT: B 260 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.4550 (m) REVERT: B 261 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7074 (mmtt) REVERT: B 263 THR cc_start: 0.8426 (m) cc_final: 0.8146 (p) REVERT: B 271 ASN cc_start: 0.7949 (t0) cc_final: 0.7219 (m-40) REVERT: B 286 SER cc_start: 0.7031 (m) cc_final: 0.6663 (m) REVERT: B 396 LYS cc_start: 0.7762 (mttt) cc_final: 0.6766 (mtpp) REVERT: B 399 LYS cc_start: 0.7035 (mtpp) cc_final: 0.6471 (mtpp) REVERT: B 415 THR cc_start: 0.7668 (p) cc_final: 0.7117 (t) REVERT: B 454 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7474 (mmtt) REVERT: B 458 ASP cc_start: 0.7835 (t0) cc_final: 0.7245 (t0) REVERT: B 475 ILE cc_start: 0.7551 (mm) cc_final: 0.7348 (mp) REVERT: B 487 LYS cc_start: 0.7966 (pttp) cc_final: 0.7559 (pttp) REVERT: B 521 ARG cc_start: 0.7463 (ppt-90) cc_final: 0.6963 (ptt-90) REVERT: B 534 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: B 553 SER cc_start: 0.8232 (m) cc_final: 0.7988 (t) REVERT: B 618 HIS cc_start: 0.7200 (m-70) cc_final: 0.6697 (m90) outliers start: 22 outliers final: 13 residues processed: 310 average time/residue: 0.3188 time to fit residues: 126.4450 Evaluate side-chains 313 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 122 LEU 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 487 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 D residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU 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 395 LEU Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 610 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 433 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** B 552 ASN ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10276 Z= 0.275 Angle : 0.772 10.857 13896 Z= 0.381 Chirality : 0.051 0.332 1550 Planarity : 0.004 0.053 1814 Dihedral : 7.334 55.619 1620 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 1.96 % Allowed : 18.12 % Favored : 79.91 % 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: -1.57 (0.24), residues: 1272 helix: -1.33 (0.82), residues: 40 sheet: -1.74 (0.72), residues: 54 loop : -1.11 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 49 HIS 0.004 0.001 HIS B 507 PHE 0.015 0.002 PHE A 436 TYR 0.019 0.002 TYR D 37 ARG 0.011 0.001 ARG A 427 *********************** 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 330 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 1.074 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 29 LYS cc_start: 0.7326 (mttp) cc_final: 0.7080 (mttp) REVERT: A 54 MET cc_start: 0.7582 (tpp) cc_final: 0.7050 (tpp) REVERT: A 58 CYS cc_start: 0.5271 (t) cc_final: 0.4864 (t) REVERT: A 59 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 78 PHE cc_start: 0.8330 (p90) cc_final: 0.8080 (p90) REVERT: A 80 LYS cc_start: 0.8531 (mttt) cc_final: 0.7869 (mtmt) REVERT: A 124 ASN cc_start: 0.8117 (m-40) cc_final: 0.7909 (m-40) REVERT: A 125 TYR cc_start: 0.8153 (p90) cc_final: 0.7652 (p90) REVERT: A 137 MET cc_start: 0.7367 (mtp) cc_final: 0.7108 (mtm) REVERT: A 149 ARG cc_start: 0.7307 (ttt90) cc_final: 0.6750 (ttt90) REVERT: A 152 ASN cc_start: 0.7467 (t0) cc_final: 0.6812 (t0) REVERT: A 171 ASP cc_start: 0.6986 (t0) cc_final: 0.6554 (t0) REVERT: A 198 SER cc_start: 0.6373 (m) cc_final: 0.6089 (t) REVERT: A 210 LEU cc_start: 0.8329 (mm) cc_final: 0.8084 (mm) REVERT: A 253 LYS cc_start: 0.8340 (mttp) cc_final: 0.8075 (mttp) REVERT: A 309 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7456 (mtm-85) REVERT: A 335 LYS cc_start: 0.7506 (tptp) cc_final: 0.7231 (tptp) REVERT: A 357 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7791 (mtmm) REVERT: A 399 LYS cc_start: 0.7115 (mtpp) cc_final: 0.6591 (mtpp) REVERT: A 405 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6883 (tp) REVERT: A 415 THR cc_start: 0.7658 (p) cc_final: 0.7163 (t) REVERT: A 426 ILE cc_start: 0.7711 (mt) cc_final: 0.7082 (tt) REVERT: A 427 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7791 (mmt90) REVERT: A 451 ARG cc_start: 0.7434 (ptp90) cc_final: 0.6147 (ptp90) REVERT: A 452 SER cc_start: 0.7403 (p) cc_final: 0.6801 (t) REVERT: A 454 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7506 (mmtt) REVERT: A 458 ASP cc_start: 0.7791 (t0) cc_final: 0.7265 (t0) REVERT: A 489 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7709 (mtmt) REVERT: A 521 ARG cc_start: 0.7617 (ppt-90) cc_final: 0.6603 (ppt-90) REVERT: A 531 ARG cc_start: 0.7012 (ttm170) cc_final: 0.6747 (ttm170) REVERT: A 548 GLU cc_start: 0.5618 (mp0) cc_final: 0.5006 (mm-30) REVERT: A 561 GLU cc_start: 0.5778 (tp30) cc_final: 0.4785 (tp30) REVERT: A 586 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6565 (tp) REVERT: A 600 MET cc_start: 0.6507 (tpp) cc_final: 0.5854 (tpp) REVERT: A 618 HIS cc_start: 0.7446 (m-70) cc_final: 0.6859 (m170) REVERT: C 15 LEU cc_start: 0.7852 (mm) cc_final: 0.7621 (mp) REVERT: D 37 TYR cc_start: 0.8380 (m-80) cc_final: 0.8145 (m-10) REVERT: B 32 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: B 54 MET cc_start: 0.7684 (tpp) cc_final: 0.7100 (tpp) REVERT: B 59 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 66 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5941 (mt-10) REVERT: B 80 LYS cc_start: 0.8526 (mttt) cc_final: 0.7874 (mttt) REVERT: B 88 TYR cc_start: 0.7533 (p90) cc_final: 0.7168 (p90) REVERT: B 111 MET cc_start: 0.7008 (ptm) cc_final: 0.6552 (ptm) REVERT: B 122 LEU cc_start: 0.7994 (mp) cc_final: 0.7690 (mt) REVERT: B 139 ASN cc_start: 0.7863 (m110) cc_final: 0.7512 (m-40) REVERT: B 149 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6686 (ttt-90) REVERT: B 168 VAL cc_start: 0.8248 (t) cc_final: 0.7893 (p) REVERT: B 171 ASP cc_start: 0.7493 (t0) cc_final: 0.6945 (t0) REVERT: B 172 PHE cc_start: 0.7978 (m-10) cc_final: 0.7382 (m-10) REVERT: B 210 LEU cc_start: 0.8296 (mm) cc_final: 0.7728 (tp) REVERT: B 213 ILE cc_start: 0.8248 (pt) cc_final: 0.8000 (pt) REVERT: B 235 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6760 (mm-40) REVERT: B 252 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6693 (ttp80) REVERT: B 260 CYS cc_start: 0.6270 (OUTLIER) cc_final: 0.4636 (m) REVERT: B 261 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7147 (mmtt) REVERT: B 263 THR cc_start: 0.8397 (m) cc_final: 0.8129 (p) REVERT: B 271 ASN cc_start: 0.7927 (t0) cc_final: 0.7168 (m-40) REVERT: B 286 SER cc_start: 0.7080 (m) cc_final: 0.6708 (m) REVERT: B 364 SER cc_start: 0.8841 (p) cc_final: 0.8447 (m) REVERT: B 399 LYS cc_start: 0.6967 (mtpp) cc_final: 0.6427 (mtpp) REVERT: B 404 PHE cc_start: 0.8002 (p90) cc_final: 0.7627 (p90) REVERT: B 415 THR cc_start: 0.7749 (p) cc_final: 0.7162 (t) REVERT: B 454 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7478 (mmtt) REVERT: B 458 ASP cc_start: 0.7843 (t0) cc_final: 0.7226 (t0) REVERT: B 475 ILE cc_start: 0.7570 (mm) cc_final: 0.7354 (mp) REVERT: B 487 LYS cc_start: 0.7930 (pttp) cc_final: 0.7492 (pttp) REVERT: B 534 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: B 553 SER cc_start: 0.8245 (m) cc_final: 0.7987 (t) REVERT: B 618 HIS cc_start: 0.7290 (m-70) cc_final: 0.6764 (m90) outliers start: 22 outliers final: 13 residues processed: 318 average time/residue: 0.3267 time to fit residues: 134.7254 Evaluate side-chains 319 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 300 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 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 D residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 534 GLU 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 73 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 chunk 125 optimal weight: 0.1980 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.0770 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN B 52 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10276 Z= 0.234 Angle : 0.767 10.869 13896 Z= 0.376 Chirality : 0.051 0.337 1550 Planarity : 0.004 0.044 1814 Dihedral : 7.186 55.340 1620 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 1.79 % Allowed : 19.20 % 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: -1.53 (0.24), residues: 1272 helix: -1.32 (0.83), residues: 40 sheet: -1.74 (0.73), residues: 54 loop : -1.08 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 49 HIS 0.009 0.001 HIS A 507 PHE 0.016 0.002 PHE A 436 TYR 0.014 0.001 TYR C 37 ARG 0.006 0.001 ARG B 98 ********************** 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 327 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7323 (mttp) cc_final: 0.7069 (mttp) REVERT: A 32 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7290 (mp-120) REVERT: A 54 MET cc_start: 0.7556 (tpp) cc_final: 0.7008 (tpp) REVERT: A 58 CYS cc_start: 0.5285 (t) cc_final: 0.4904 (t) REVERT: A 59 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 78 PHE cc_start: 0.8309 (p90) cc_final: 0.8039 (p90) REVERT: A 80 LYS cc_start: 0.8513 (mttt) cc_final: 0.7914 (mtmt) REVERT: A 124 ASN cc_start: 0.8110 (m-40) cc_final: 0.7875 (m-40) REVERT: A 125 TYR cc_start: 0.8135 (p90) cc_final: 0.7602 (p90) REVERT: A 137 MET cc_start: 0.7376 (mtp) cc_final: 0.7100 (mtm) REVERT: A 149 ARG cc_start: 0.7329 (ttt90) cc_final: 0.6679 (ttt-90) REVERT: A 152 ASN cc_start: 0.7465 (t0) cc_final: 0.6778 (t0) REVERT: A 171 ASP cc_start: 0.6932 (t0) cc_final: 0.6630 (t0) REVERT: A 198 SER cc_start: 0.6505 (m) cc_final: 0.6223 (t) REVERT: A 210 LEU cc_start: 0.8332 (mm) cc_final: 0.8089 (mm) REVERT: A 253 LYS cc_start: 0.8317 (mttp) cc_final: 0.8036 (mttp) REVERT: A 309 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7514 (mtt90) REVERT: A 335 LYS cc_start: 0.7521 (tptp) cc_final: 0.7255 (tptp) REVERT: A 357 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7800 (mtmm) REVERT: A 399 LYS cc_start: 0.7081 (mtpp) cc_final: 0.6567 (mtpp) REVERT: A 405 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7005 (tp) REVERT: A 415 THR cc_start: 0.7657 (p) cc_final: 0.7164 (t) REVERT: A 427 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7770 (mmt90) REVERT: A 451 ARG cc_start: 0.7399 (ptp90) cc_final: 0.6424 (ptp90) REVERT: A 452 SER cc_start: 0.7351 (p) cc_final: 0.6607 (t) REVERT: A 454 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7419 (mmtt) REVERT: A 458 ASP cc_start: 0.7873 (t0) cc_final: 0.7384 (t0) REVERT: A 521 ARG cc_start: 0.7638 (ppt-90) cc_final: 0.6971 (ppt-90) REVERT: A 522 ASP cc_start: 0.7022 (m-30) cc_final: 0.5986 (t0) REVERT: A 531 ARG cc_start: 0.7004 (ttm170) cc_final: 0.6702 (ttm170) REVERT: A 548 GLU cc_start: 0.5591 (mp0) cc_final: 0.4910 (mm-30) REVERT: A 561 GLU cc_start: 0.5801 (tp30) cc_final: 0.5408 (mm-30) REVERT: A 586 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6545 (tp) REVERT: A 600 MET cc_start: 0.6519 (tpp) cc_final: 0.5875 (tpp) REVERT: A 618 HIS cc_start: 0.7516 (m-70) cc_final: 0.7019 (m-70) REVERT: C 15 LEU cc_start: 0.7871 (mm) cc_final: 0.7649 (mp) REVERT: D 37 TYR cc_start: 0.8347 (m-80) cc_final: 0.8115 (m-10) REVERT: D 49 TRP cc_start: 0.7659 (m-10) cc_final: 0.7348 (m-10) REVERT: B 32 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: B 54 MET cc_start: 0.7594 (tpp) cc_final: 0.7058 (tpp) REVERT: B 59 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7262 (mt-10) REVERT: B 66 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6017 (mt-10) REVERT: B 80 LYS cc_start: 0.8515 (mttt) cc_final: 0.7873 (mttt) REVERT: B 88 TYR cc_start: 0.7537 (p90) cc_final: 0.7183 (p90) REVERT: B 111 MET cc_start: 0.6955 (ptm) cc_final: 0.6508 (ptm) REVERT: B 139 ASN cc_start: 0.7898 (m110) cc_final: 0.7618 (m-40) REVERT: B 149 ARG cc_start: 0.7306 (ttt90) cc_final: 0.6717 (ttt-90) REVERT: B 168 VAL cc_start: 0.8252 (t) cc_final: 0.7893 (p) REVERT: B 171 ASP cc_start: 0.7481 (t0) cc_final: 0.6930 (t0) REVERT: B 172 PHE cc_start: 0.7871 (m-10) cc_final: 0.7278 (m-10) REVERT: B 210 LEU cc_start: 0.8284 (mm) cc_final: 0.7693 (tp) REVERT: B 213 ILE cc_start: 0.8219 (pt) cc_final: 0.7962 (pt) REVERT: B 235 GLN cc_start: 0.7403 (mm-40) cc_final: 0.6796 (mm-40) REVERT: B 252 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6774 (ttp80) REVERT: B 260 CYS cc_start: 0.6212 (OUTLIER) cc_final: 0.4679 (m) REVERT: B 261 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7075 (mmtt) REVERT: B 263 THR cc_start: 0.8381 (m) cc_final: 0.8129 (p) REVERT: B 271 ASN cc_start: 0.7931 (t0) cc_final: 0.7172 (m-40) REVERT: B 286 SER cc_start: 0.7036 (m) cc_final: 0.6695 (m) REVERT: B 364 SER cc_start: 0.8840 (p) cc_final: 0.8433 (m) REVERT: B 399 LYS cc_start: 0.7028 (mtpp) cc_final: 0.6479 (mtpp) REVERT: B 454 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7481 (mmtt) REVERT: B 458 ASP cc_start: 0.7832 (t0) cc_final: 0.7247 (t0) REVERT: B 487 LYS cc_start: 0.7921 (pttp) cc_final: 0.7478 (pttp) REVERT: B 534 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: B 553 SER cc_start: 0.8246 (m) cc_final: 0.7995 (t) REVERT: B 561 GLU cc_start: 0.6815 (tp30) cc_final: 0.5600 (tm-30) REVERT: B 618 HIS cc_start: 0.7302 (m-70) cc_final: 0.6754 (m90) outliers start: 20 outliers final: 11 residues processed: 316 average time/residue: 0.3100 time to fit residues: 126.2087 Evaluate side-chains 324 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 307 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 487 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 D residue 50 TRP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 534 GLU 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 30 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 486 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131465 restraints weight = 14828.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135791 restraints weight = 7535.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138706 restraints weight = 4575.220| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10276 Z= 0.317 Angle : 0.784 10.721 13896 Z= 0.391 Chirality : 0.052 0.331 1550 Planarity : 0.004 0.046 1814 Dihedral : 7.220 55.165 1620 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.49 % Favored : 91.43 % Rotamer: Outliers : 1.96 % Allowed : 19.20 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (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: -1.60 (0.24), residues: 1272 helix: -1.06 (0.86), residues: 38 sheet: -1.77 (0.73), residues: 54 loop : -1.14 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.017 0.002 PHE A 287 TYR 0.017 0.002 TYR D 37 ARG 0.007 0.001 ARG A 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.64 seconds wall clock time: 54 minutes 29.79 seconds (3269.79 seconds total)