Starting phenix.real_space_refine on Thu Mar 13 00:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9n_36111/03_2025/8j9n_36111.cif" } resolution = 3.5 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5396 2.51 5 N 1461 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8483 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 356, 2761 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 356, 2761 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 2827 Chain: "C" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2500 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 380 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 944 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 322 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 322 " occ=0.50 Time building chain proxies: 6.20, per 1000 atoms: 0.73 Number of scatterers: 8483 At special positions: 0 Unit cell: (76.32, 98.58, 150.52, 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 55 16.00 O 1571 8.00 N 1461 7.00 C 5396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 402 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS N 45 " - pdb=" SG CYS N 119 " distance=2.04 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 130 " 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 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 37.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.603A pdb=" N LYS B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 344 removed outlier: 3.594A pdb=" N LEU B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP B 326 " --> pdb=" O ATRP B 322 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 376 removed outlier: 4.368A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 365 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 432 removed outlier: 3.838A pdb=" N ALA B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 466 removed outlier: 4.330A pdb=" N VAL B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 491 through 524 Processing helix chain 'B' and resid 527 through 573 removed outlier: 3.540A pdb=" N TYR B 544 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 3.509A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.891A pdb=" N PHE B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.972A pdb=" N ILE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.931A pdb=" N TRP B 620 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 636 removed outlier: 3.631A pdb=" N LEU B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 635 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 removed outlier: 3.673A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.552A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 No H-bonds generated for 'chain 'C' and resid 253 through 265' Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.828A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.752A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.220A pdb=" N TYR C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 3.987A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 331 through 353 removed outlier: 3.537A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 391 removed outlier: 3.640A pdb=" N TYR C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 26 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.883A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 47 removed outlier: 3.950A pdb=" N ALA E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'N' and resid 110 through 114 removed outlier: 3.829A pdb=" N THR N 114 " --> pdb=" O PRO N 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.585A pdb=" N LEU C 43 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL C 224 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 52 removed outlier: 7.108A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 4.051A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 70 " --> pdb=" O TRP D 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.783A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.845A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 203 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 233 removed outlier: 3.658A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.686A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS D 294 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 308 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 26 through 29 removed outlier: 3.552A pdb=" N ASP N 96 " --> pdb=" O THR N 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 68 through 69 357 hydrogen bonds defined for protein. 1030 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: 2.24 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2768 1.34 - 1.46: 2069 1.46 - 1.58: 3763 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8676 Sorted by residual: bond pdb=" N PRO B 598 " pdb=" CD PRO B 598 " ideal model delta sigma weight residual 1.473 1.537 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C ALA B 493 " pdb=" N PRO B 494 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.77e+00 bond pdb=" N THR D 196 " pdb=" CA THR D 196 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.47e+00 bond pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB GLN D 17 " pdb=" CG GLN D 17 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 11748 4.84 - 9.68: 44 9.68 - 14.52: 3 14.52 - 19.37: 1 19.37 - 24.21: 1 Bond angle restraints: 11797 Sorted by residual: angle pdb=" CA LEU B 608 " pdb=" CB LEU B 608 " pdb=" CG LEU B 608 " ideal model delta sigma weight residual 116.30 140.51 -24.21 3.50e+00 8.16e-02 4.78e+01 angle pdb=" CB MET B 609 " pdb=" CG MET B 609 " pdb=" SD MET B 609 " ideal model delta sigma weight residual 112.70 130.78 -18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" N PRO B 598 " pdb=" CA PRO B 598 " pdb=" C PRO B 598 " ideal model delta sigma weight residual 111.77 102.54 9.23 1.67e+00 3.59e-01 3.06e+01 angle pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " pdb=" CG LEU B 291 " ideal model delta sigma weight residual 116.30 130.42 -14.12 3.50e+00 8.16e-02 1.63e+01 angle pdb=" C LYS B 294 " pdb=" N ASP B 295 " pdb=" CA ASP B 295 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4581 16.61 - 33.22: 394 33.22 - 49.82: 99 49.82 - 66.43: 19 66.43 - 83.04: 7 Dihedral angle restraints: 5100 sinusoidal: 1889 harmonic: 3211 Sorted by residual: dihedral pdb=" CA LEU B 608 " pdb=" C LEU B 608 " pdb=" N MET B 609 " pdb=" CA MET B 609 " ideal model delta harmonic sigma weight residual 180.00 -144.88 -35.12 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CB CYS B 402 " pdb=" SG CYS B 402 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -140.88 54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS B 276 " pdb=" SG CYS B 276 " pdb=" SG CYS B 296 " pdb=" CB CYS B 296 " ideal model delta sinusoidal sigma weight residual -86.00 -139.85 53.85 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 958 0.049 - 0.098: 286 0.098 - 0.147: 74 0.147 - 0.197: 9 0.197 - 0.246: 3 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CB ILE D 43 " pdb=" CA ILE D 43 " pdb=" CG1 ILE D 43 " pdb=" CG2 ILE D 43 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 440 " pdb=" CA ILE B 440 " pdb=" CG1 ILE B 440 " pdb=" CG2 ILE B 440 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1327 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 597 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO B 598 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 597 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C SER B 597 " -0.053 2.00e-02 2.50e+03 pdb=" O SER B 597 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO B 598 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 331 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 332 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 332 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 332 " 0.037 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1733 2.78 - 3.31: 7916 3.31 - 3.84: 13951 3.84 - 4.37: 15682 4.37 - 4.90: 27304 Nonbonded interactions: 66586 Sorted by model distance: nonbonded pdb=" OH TYR C 318 " pdb=" OD2 ASP C 343 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 327 " pdb=" O ALA B 366 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 410 " pdb=" NZ LYS B 458 " model vdw 2.256 3.120 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.273 3.040 nonbonded pdb=" O GLU B 441 " pdb=" OG SER B 444 " model vdw 2.290 3.040 ... (remaining 66581 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.080 Find NCS groups from input model: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.064 8676 Z= 0.249 Angle : 0.869 24.207 11797 Z= 0.431 Chirality : 0.050 0.246 1330 Planarity : 0.006 0.122 1509 Dihedral : 13.711 83.038 3015 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1096 helix: 0.20 (0.26), residues: 387 sheet: -0.79 (0.35), residues: 226 loop : -2.10 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 63 HIS 0.005 0.001 HIS C 220 PHE 0.035 0.002 PHE B 600 TYR 0.035 0.002 TYR B 498 ARG 0.012 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 441 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6338 (mm-30) REVERT: B 500 PHE cc_start: 0.6938 (t80) cc_final: 0.6717 (t80) REVERT: B 558 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6002 (mm-30) REVERT: C 274 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7644 (ttpt) REVERT: C 295 ASP cc_start: 0.7412 (m-30) cc_final: 0.7000 (m-30) REVERT: C 300 LYS cc_start: 0.7912 (tttm) cc_final: 0.7569 (tttp) REVERT: C 382 THR cc_start: 0.8087 (m) cc_final: 0.7876 (m) REVERT: D 148 CYS cc_start: 0.7766 (t) cc_final: 0.7388 (t) REVERT: D 163 ASP cc_start: 0.6613 (p0) cc_final: 0.6225 (p0) REVERT: D 188 MET cc_start: 0.7132 (mmm) cc_final: 0.6564 (mmm) REVERT: D 204 CYS cc_start: 0.7468 (m) cc_final: 0.7172 (m) REVERT: D 280 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7882 (mtpp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2533 time to fit residues: 78.7083 Evaluate side-chains 223 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 88 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS N 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123957 restraints weight = 13032.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127952 restraints weight = 6473.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130633 restraints weight = 3939.458| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8676 Z= 0.253 Angle : 0.666 18.399 11797 Z= 0.340 Chirality : 0.044 0.190 1330 Planarity : 0.005 0.065 1509 Dihedral : 4.689 23.844 1201 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.38 % Allowed : 9.63 % Favored : 88.99 % 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: -1.11 (0.25), residues: 1096 helix: 0.87 (0.28), residues: 385 sheet: -0.91 (0.35), residues: 235 loop : -2.02 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 420 HIS 0.004 0.001 HIS C 220 PHE 0.031 0.002 PHE C 212 TYR 0.026 0.002 TYR B 498 ARG 0.006 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.7123 (ttt) cc_final: 0.6903 (ttt) REVERT: B 500 PHE cc_start: 0.7106 (t80) cc_final: 0.6866 (t80) REVERT: B 505 PHE cc_start: 0.7838 (m-10) cc_final: 0.7635 (m-10) REVERT: B 554 CYS cc_start: 0.7588 (t) cc_final: 0.7153 (t) REVERT: B 558 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6127 (mm-30) REVERT: C 212 PHE cc_start: 0.6946 (p90) cc_final: 0.6663 (p90) REVERT: C 221 MET cc_start: 0.7369 (ttm) cc_final: 0.7127 (ttm) REVERT: C 274 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7533 (ttpt) REVERT: C 295 ASP cc_start: 0.7586 (m-30) cc_final: 0.7121 (m-30) REVERT: C 341 ILE cc_start: 0.7322 (mm) cc_final: 0.7109 (mt) REVERT: C 381 ASP cc_start: 0.7837 (t70) cc_final: 0.7267 (t0) REVERT: C 382 THR cc_start: 0.8116 (m) cc_final: 0.7906 (m) REVERT: D 65 THR cc_start: 0.8372 (p) cc_final: 0.8145 (p) REVERT: D 111 TYR cc_start: 0.8215 (m-80) cc_final: 0.7892 (m-80) REVERT: D 118 ASP cc_start: 0.7253 (p0) cc_final: 0.6983 (p0) REVERT: D 121 CYS cc_start: 0.7705 (t) cc_final: 0.7317 (t) REVERT: D 143 THR cc_start: 0.8072 (p) cc_final: 0.7781 (t) REVERT: D 148 CYS cc_start: 0.7944 (t) cc_final: 0.7554 (t) REVERT: D 177 THR cc_start: 0.8199 (m) cc_final: 0.7991 (t) REVERT: D 188 MET cc_start: 0.7351 (mmm) cc_final: 0.6844 (mmm) REVERT: D 204 CYS cc_start: 0.7617 (m) cc_final: 0.7230 (m) REVERT: D 277 SER cc_start: 0.7700 (t) cc_final: 0.7465 (t) REVERT: D 284 LEU cc_start: 0.7938 (tp) cc_final: 0.7715 (tt) REVERT: D 298 ASP cc_start: 0.8041 (t70) cc_final: 0.7781 (t0) outliers start: 12 outliers final: 9 residues processed: 243 average time/residue: 0.2492 time to fit residues: 78.6887 Evaluate side-chains 243 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 234 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124269 restraints weight = 13132.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128305 restraints weight = 6507.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131021 restraints weight = 3948.642| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8676 Z= 0.233 Angle : 0.626 19.537 11797 Z= 0.321 Chirality : 0.043 0.186 1330 Planarity : 0.005 0.058 1509 Dihedral : 4.559 21.284 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.06 % Allowed : 13.88 % Favored : 84.06 % 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: -0.97 (0.26), residues: 1096 helix: 1.09 (0.28), residues: 386 sheet: -0.88 (0.35), residues: 234 loop : -2.01 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.035 0.002 PHE B 540 TYR 0.027 0.002 TYR B 544 ARG 0.008 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6734 (mmt) cc_final: 0.6223 (mmt) REVERT: B 408 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7148 (ttt) REVERT: B 496 PHE cc_start: 0.7588 (t80) cc_final: 0.7250 (t80) REVERT: B 500 PHE cc_start: 0.7161 (t80) cc_final: 0.6904 (t80) REVERT: B 558 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6124 (mm-30) REVERT: C 30 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7297 (tpp80) REVERT: C 212 PHE cc_start: 0.7017 (p90) cc_final: 0.6697 (p90) REVERT: C 221 MET cc_start: 0.7403 (ttm) cc_final: 0.7017 (ttm) REVERT: C 274 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7541 (ttpt) REVERT: C 295 ASP cc_start: 0.7647 (m-30) cc_final: 0.7155 (m-30) REVERT: C 336 ARG cc_start: 0.6363 (ttp80) cc_final: 0.6110 (mtp85) REVERT: C 381 ASP cc_start: 0.7848 (t70) cc_final: 0.7206 (t0) REVERT: D 65 THR cc_start: 0.8431 (p) cc_final: 0.8173 (p) REVERT: D 118 ASP cc_start: 0.7262 (p0) cc_final: 0.6988 (p0) REVERT: D 121 CYS cc_start: 0.7719 (t) cc_final: 0.7346 (t) REVERT: D 143 THR cc_start: 0.8126 (p) cc_final: 0.7780 (t) REVERT: D 148 CYS cc_start: 0.7937 (t) cc_final: 0.7526 (t) REVERT: D 188 MET cc_start: 0.7379 (mmm) cc_final: 0.6894 (mmm) REVERT: D 204 CYS cc_start: 0.7690 (m) cc_final: 0.7265 (m) REVERT: D 277 SER cc_start: 0.7750 (t) cc_final: 0.7486 (t) REVERT: D 284 LEU cc_start: 0.7991 (tp) cc_final: 0.7586 (tp) REVERT: D 304 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7720 (ptm160) REVERT: E 45 MET cc_start: 0.5297 (tmm) cc_final: 0.5018 (tmm) outliers start: 18 outliers final: 13 residues processed: 237 average time/residue: 0.2582 time to fit residues: 79.5066 Evaluate side-chains 247 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125571 restraints weight = 13179.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129506 restraints weight = 6648.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132123 restraints weight = 4082.484| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8676 Z= 0.180 Angle : 0.618 20.051 11797 Z= 0.308 Chirality : 0.042 0.177 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.389 21.126 1201 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.87 % Allowed : 14.68 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.26), residues: 1096 helix: 1.21 (0.28), residues: 385 sheet: -0.87 (0.35), residues: 234 loop : -1.93 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 420 HIS 0.003 0.001 HIS C 220 PHE 0.032 0.001 PHE B 540 TYR 0.024 0.001 TYR B 544 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 GLU cc_start: 0.7443 (tp30) cc_final: 0.7213 (tp30) REVERT: B 407 MET cc_start: 0.6684 (mmt) cc_final: 0.6222 (mmt) REVERT: B 496 PHE cc_start: 0.7515 (t80) cc_final: 0.7208 (t80) REVERT: B 505 PHE cc_start: 0.7788 (m-10) cc_final: 0.7558 (m-10) REVERT: B 554 CYS cc_start: 0.7453 (t) cc_final: 0.7030 (t) REVERT: B 558 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6012 (mm-30) REVERT: C 15 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6438 (tp30) REVERT: C 212 PHE cc_start: 0.6952 (p90) cc_final: 0.6662 (p90) REVERT: C 221 MET cc_start: 0.7326 (ttm) cc_final: 0.6986 (ttm) REVERT: C 274 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7579 (ttpt) REVERT: C 295 ASP cc_start: 0.7467 (m-30) cc_final: 0.7005 (m-30) REVERT: C 336 ARG cc_start: 0.6288 (ttp80) cc_final: 0.6081 (mtp85) REVERT: C 338 LYS cc_start: 0.8299 (tttm) cc_final: 0.7954 (tttm) REVERT: C 381 ASP cc_start: 0.7815 (t70) cc_final: 0.7128 (t0) REVERT: D 17 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 65 THR cc_start: 0.8426 (p) cc_final: 0.8163 (p) REVERT: D 111 TYR cc_start: 0.8145 (m-80) cc_final: 0.7830 (m-80) REVERT: D 118 ASP cc_start: 0.7166 (p0) cc_final: 0.6896 (p0) REVERT: D 121 CYS cc_start: 0.7598 (t) cc_final: 0.7280 (t) REVERT: D 143 THR cc_start: 0.8077 (p) cc_final: 0.7746 (t) REVERT: D 148 CYS cc_start: 0.7859 (t) cc_final: 0.7456 (t) REVERT: D 188 MET cc_start: 0.7225 (mmm) cc_final: 0.6679 (mmm) REVERT: D 204 CYS cc_start: 0.7577 (m) cc_final: 0.7167 (m) REVERT: D 277 SER cc_start: 0.7706 (t) cc_final: 0.7456 (t) REVERT: D 284 LEU cc_start: 0.7970 (tp) cc_final: 0.7575 (tp) outliers start: 25 outliers final: 19 residues processed: 240 average time/residue: 0.2580 time to fit residues: 80.2497 Evaluate side-chains 255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 34 optimal weight: 0.0010 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.0000 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS D 259 GLN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126097 restraints weight = 12973.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130077 restraints weight = 6459.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132768 restraints weight = 3952.104| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8676 Z= 0.169 Angle : 0.605 19.265 11797 Z= 0.301 Chirality : 0.042 0.161 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.257 19.925 1201 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.10 % Allowed : 14.45 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.26), residues: 1096 helix: 1.40 (0.28), residues: 383 sheet: -0.87 (0.35), residues: 238 loop : -1.87 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 620 HIS 0.004 0.001 HIS C 220 PHE 0.021 0.001 PHE C 212 TYR 0.019 0.001 TYR B 498 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 GLU cc_start: 0.7432 (tp30) cc_final: 0.7142 (tp30) REVERT: B 407 MET cc_start: 0.6664 (mmt) cc_final: 0.6181 (mmt) REVERT: B 408 MET cc_start: 0.7494 (ttt) cc_final: 0.7256 (ttp) REVERT: B 496 PHE cc_start: 0.7545 (t80) cc_final: 0.7192 (t80) REVERT: B 554 CYS cc_start: 0.7564 (t) cc_final: 0.7070 (t) REVERT: B 558 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6020 (mm-30) REVERT: C 212 PHE cc_start: 0.7020 (p90) cc_final: 0.6771 (p90) REVERT: C 221 MET cc_start: 0.7392 (ttm) cc_final: 0.7014 (ttm) REVERT: C 274 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7559 (ttpt) REVERT: C 295 ASP cc_start: 0.7590 (m-30) cc_final: 0.7080 (m-30) REVERT: C 336 ARG cc_start: 0.6330 (ttp80) cc_final: 0.6128 (mtp85) REVERT: C 381 ASP cc_start: 0.7797 (t70) cc_final: 0.7388 (t70) REVERT: C 385 GLN cc_start: 0.8192 (tp40) cc_final: 0.7840 (mm-40) REVERT: D 17 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 65 THR cc_start: 0.8430 (p) cc_final: 0.8172 (p) REVERT: D 111 TYR cc_start: 0.8148 (m-80) cc_final: 0.7804 (m-80) REVERT: D 118 ASP cc_start: 0.7242 (p0) cc_final: 0.7001 (p0) REVERT: D 121 CYS cc_start: 0.7710 (t) cc_final: 0.7421 (t) REVERT: D 137 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6635 (tpp-160) REVERT: D 143 THR cc_start: 0.8082 (p) cc_final: 0.7580 (t) REVERT: D 148 CYS cc_start: 0.7891 (t) cc_final: 0.7489 (t) REVERT: D 188 MET cc_start: 0.7325 (mmm) cc_final: 0.6665 (mmm) REVERT: D 204 CYS cc_start: 0.7657 (m) cc_final: 0.7233 (m) REVERT: D 277 SER cc_start: 0.7787 (t) cc_final: 0.7514 (t) REVERT: D 284 LEU cc_start: 0.7969 (tp) cc_final: 0.7529 (tp) REVERT: N 106 MET cc_start: 0.6707 (mmm) cc_final: 0.6309 (tpp) outliers start: 27 outliers final: 21 residues processed: 247 average time/residue: 0.2864 time to fit residues: 91.8272 Evaluate side-chains 257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123790 restraints weight = 12995.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127713 restraints weight = 6654.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130352 restraints weight = 4112.048| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8676 Z= 0.257 Angle : 0.612 14.156 11797 Z= 0.317 Chirality : 0.043 0.160 1330 Planarity : 0.004 0.056 1509 Dihedral : 4.417 25.571 1201 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.75 % Allowed : 15.60 % Favored : 81.65 % 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: -0.74 (0.26), residues: 1096 helix: 1.40 (0.28), residues: 383 sheet: -0.86 (0.35), residues: 236 loop : -1.90 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 620 HIS 0.004 0.001 HIS D 183 PHE 0.025 0.002 PHE B 540 TYR 0.023 0.002 TYR B 498 ARG 0.005 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6571 (mmt) cc_final: 0.6167 (mmt) REVERT: B 496 PHE cc_start: 0.7498 (t80) cc_final: 0.7250 (t80) REVERT: B 558 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5997 (mm-30) REVERT: C 274 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7624 (ttpt) REVERT: C 295 ASP cc_start: 0.7438 (m-30) cc_final: 0.7182 (m-30) REVERT: C 336 ARG cc_start: 0.6393 (ttp80) cc_final: 0.6164 (mtp85) REVERT: C 338 LYS cc_start: 0.8339 (tttm) cc_final: 0.8107 (tttm) REVERT: C 381 ASP cc_start: 0.7819 (t70) cc_final: 0.7015 (t0) REVERT: C 385 GLN cc_start: 0.8141 (tp40) cc_final: 0.7836 (mm-40) REVERT: D 65 THR cc_start: 0.8461 (p) cc_final: 0.8197 (p) REVERT: D 118 ASP cc_start: 0.7181 (p0) cc_final: 0.6938 (p0) REVERT: D 121 CYS cc_start: 0.7593 (t) cc_final: 0.7350 (t) REVERT: D 137 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6813 (tpp-160) REVERT: D 143 THR cc_start: 0.7981 (p) cc_final: 0.7757 (t) REVERT: D 148 CYS cc_start: 0.7819 (t) cc_final: 0.7493 (t) REVERT: D 163 ASP cc_start: 0.7358 (p0) cc_final: 0.6904 (p0) REVERT: D 188 MET cc_start: 0.7203 (mmm) cc_final: 0.6674 (mmm) REVERT: D 204 CYS cc_start: 0.7605 (m) cc_final: 0.7212 (m) REVERT: D 277 SER cc_start: 0.7671 (t) cc_final: 0.7417 (t) REVERT: D 284 LEU cc_start: 0.8008 (tp) cc_final: 0.7590 (tp) REVERT: N 106 MET cc_start: 0.6680 (mmm) cc_final: 0.6340 (tpp) outliers start: 24 outliers final: 23 residues processed: 241 average time/residue: 0.2577 time to fit residues: 80.0349 Evaluate side-chains 253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS D 259 GLN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124044 restraints weight = 13056.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128248 restraints weight = 6447.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130963 restraints weight = 3907.835| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.207 Angle : 0.616 13.652 11797 Z= 0.316 Chirality : 0.043 0.158 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.400 26.878 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.98 % Allowed : 17.09 % Favored : 79.93 % 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: -0.65 (0.26), residues: 1096 helix: 1.48 (0.28), residues: 383 sheet: -0.79 (0.36), residues: 232 loop : -1.86 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 427 HIS 0.003 0.001 HIS D 183 PHE 0.022 0.001 PHE B 540 TYR 0.023 0.001 TYR B 498 ARG 0.009 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6550 (mmt) cc_final: 0.6069 (mmt) REVERT: B 496 PHE cc_start: 0.7504 (t80) cc_final: 0.7253 (t80) REVERT: C 15 GLU cc_start: 0.6906 (tp30) cc_final: 0.6542 (tp30) REVERT: C 221 MET cc_start: 0.7376 (ttm) cc_final: 0.7162 (ttm) REVERT: C 274 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7594 (ttpt) REVERT: C 295 ASP cc_start: 0.7545 (m-30) cc_final: 0.6903 (m-30) REVERT: C 336 ARG cc_start: 0.6389 (ttp80) cc_final: 0.6167 (mtp85) REVERT: C 338 LYS cc_start: 0.8240 (tttm) cc_final: 0.7997 (tttm) REVERT: C 381 ASP cc_start: 0.7818 (t70) cc_final: 0.7011 (t0) REVERT: D 65 THR cc_start: 0.8454 (p) cc_final: 0.8190 (p) REVERT: D 118 ASP cc_start: 0.7155 (p0) cc_final: 0.6902 (p0) REVERT: D 121 CYS cc_start: 0.7650 (t) cc_final: 0.7383 (t) REVERT: D 137 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6828 (tpp-160) REVERT: D 143 THR cc_start: 0.8011 (p) cc_final: 0.7626 (t) REVERT: D 148 CYS cc_start: 0.7850 (t) cc_final: 0.7533 (t) REVERT: D 188 MET cc_start: 0.7279 (mmm) cc_final: 0.6815 (mmm) REVERT: D 198 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7667 (mt) REVERT: D 204 CYS cc_start: 0.7621 (m) cc_final: 0.7224 (m) REVERT: D 277 SER cc_start: 0.7724 (t) cc_final: 0.7435 (t) REVERT: D 284 LEU cc_start: 0.8003 (tp) cc_final: 0.7540 (tp) REVERT: N 106 MET cc_start: 0.6732 (mmm) cc_final: 0.6424 (tpp) outliers start: 26 outliers final: 23 residues processed: 241 average time/residue: 0.2884 time to fit residues: 90.2545 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS D 259 GLN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125377 restraints weight = 13141.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129351 restraints weight = 6698.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132004 restraints weight = 4137.908| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.194 Angle : 0.618 14.674 11797 Z= 0.315 Chirality : 0.042 0.157 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.362 25.689 1201 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.98 % Allowed : 17.66 % Favored : 79.36 % 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: -0.62 (0.26), residues: 1096 helix: 1.49 (0.28), residues: 383 sheet: -0.76 (0.36), residues: 237 loop : -1.85 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 420 HIS 0.003 0.001 HIS C 220 PHE 0.021 0.001 PHE B 540 TYR 0.025 0.001 TYR B 498 ARG 0.008 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 THR cc_start: 0.8275 (m) cc_final: 0.7766 (p) REVERT: B 407 MET cc_start: 0.6533 (mmt) cc_final: 0.6077 (mmt) REVERT: B 496 PHE cc_start: 0.7426 (t80) cc_final: 0.7218 (t80) REVERT: C 221 MET cc_start: 0.7269 (ttm) cc_final: 0.7023 (ttp) REVERT: C 274 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7608 (ttpt) REVERT: C 336 ARG cc_start: 0.6330 (ttp80) cc_final: 0.6129 (mtp85) REVERT: C 338 LYS cc_start: 0.8300 (tttm) cc_final: 0.8090 (tttm) REVERT: C 381 ASP cc_start: 0.7807 (t70) cc_final: 0.7016 (t0) REVERT: D 65 THR cc_start: 0.8461 (p) cc_final: 0.8193 (p) REVERT: D 111 TYR cc_start: 0.8149 (m-80) cc_final: 0.7865 (m-80) REVERT: D 118 ASP cc_start: 0.7056 (p0) cc_final: 0.6811 (p0) REVERT: D 121 CYS cc_start: 0.7547 (t) cc_final: 0.7327 (t) REVERT: D 143 THR cc_start: 0.8006 (p) cc_final: 0.7703 (t) REVERT: D 148 CYS cc_start: 0.7816 (t) cc_final: 0.7482 (t) REVERT: D 163 ASP cc_start: 0.7237 (p0) cc_final: 0.6874 (p0) REVERT: D 188 MET cc_start: 0.7109 (mmm) cc_final: 0.6628 (mmm) REVERT: D 198 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7682 (mt) REVERT: D 204 CYS cc_start: 0.7551 (m) cc_final: 0.7174 (m) REVERT: D 234 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7119 (t80) REVERT: D 277 SER cc_start: 0.7644 (t) cc_final: 0.7389 (t) REVERT: D 284 LEU cc_start: 0.7982 (tp) cc_final: 0.7583 (tp) REVERT: N 106 MET cc_start: 0.6659 (mmm) cc_final: 0.6399 (tpp) outliers start: 26 outliers final: 22 residues processed: 247 average time/residue: 0.2594 time to fit residues: 82.7278 Evaluate side-chains 257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.0170 chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 86 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN N 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125799 restraints weight = 13192.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129777 restraints weight = 6701.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132437 restraints weight = 4129.686| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.182 Angle : 0.618 15.018 11797 Z= 0.314 Chirality : 0.042 0.156 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.317 25.816 1201 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 2.98 % Allowed : 18.12 % Favored : 78.90 % 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: -0.57 (0.26), residues: 1096 helix: 1.52 (0.28), residues: 385 sheet: -0.76 (0.36), residues: 237 loop : -1.81 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 620 HIS 0.004 0.001 HIS C 220 PHE 0.020 0.001 PHE B 540 TYR 0.027 0.001 TYR B 498 ARG 0.008 0.000 ARG D 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 PHE cc_start: 0.8207 (t80) cc_final: 0.7903 (t80) REVERT: B 407 MET cc_start: 0.6548 (mmt) cc_final: 0.6107 (mmt) REVERT: C 221 MET cc_start: 0.7265 (ttm) cc_final: 0.7014 (ttp) REVERT: C 274 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7613 (ttpt) REVERT: C 295 ASP cc_start: 0.7711 (m-30) cc_final: 0.7085 (m-30) REVERT: C 336 ARG cc_start: 0.6311 (ttp80) cc_final: 0.6106 (mtp85) REVERT: C 338 LYS cc_start: 0.8277 (tttm) cc_final: 0.8054 (tttm) REVERT: C 381 ASP cc_start: 0.7806 (t70) cc_final: 0.7383 (t70) REVERT: D 61 MET cc_start: 0.7412 (ppp) cc_final: 0.6786 (ppp) REVERT: D 65 THR cc_start: 0.8454 (p) cc_final: 0.8177 (p) REVERT: D 111 TYR cc_start: 0.8140 (m-80) cc_final: 0.7862 (m-80) REVERT: D 118 ASP cc_start: 0.7067 (p0) cc_final: 0.6833 (p0) REVERT: D 121 CYS cc_start: 0.7548 (t) cc_final: 0.7337 (t) REVERT: D 143 THR cc_start: 0.8012 (p) cc_final: 0.7710 (t) REVERT: D 148 CYS cc_start: 0.7830 (t) cc_final: 0.7509 (t) REVERT: D 163 ASP cc_start: 0.7201 (p0) cc_final: 0.6839 (p0) REVERT: D 188 MET cc_start: 0.7100 (mmm) cc_final: 0.6644 (mmm) REVERT: D 198 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (mt) REVERT: D 204 CYS cc_start: 0.7551 (m) cc_final: 0.7165 (m) REVERT: D 234 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.6942 (t80) REVERT: D 277 SER cc_start: 0.7632 (t) cc_final: 0.7390 (t) REVERT: D 284 LEU cc_start: 0.7975 (tp) cc_final: 0.7567 (tp) REVERT: N 106 MET cc_start: 0.6779 (mmm) cc_final: 0.6557 (tpp) outliers start: 26 outliers final: 23 residues processed: 241 average time/residue: 0.2696 time to fit residues: 84.2825 Evaluate side-chains 255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0060 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126586 restraints weight = 13119.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130669 restraints weight = 6530.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133347 restraints weight = 3965.628| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8676 Z= 0.163 Angle : 0.611 14.699 11797 Z= 0.311 Chirality : 0.042 0.179 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.236 26.321 1201 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 2.98 % Allowed : 18.69 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.26), residues: 1096 helix: 1.59 (0.28), residues: 385 sheet: -0.69 (0.35), residues: 241 loop : -1.81 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 420 HIS 0.003 0.001 HIS C 220 PHE 0.021 0.001 PHE B 540 TYR 0.029 0.001 TYR B 498 ARG 0.007 0.000 ARG D 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6576 (mmt) cc_final: 0.6083 (mmt) REVERT: C 221 MET cc_start: 0.7366 (ttm) cc_final: 0.7024 (ttp) REVERT: C 274 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7572 (ttpt) REVERT: C 295 ASP cc_start: 0.7863 (m-30) cc_final: 0.7261 (m-30) REVERT: C 300 LYS cc_start: 0.7812 (tttm) cc_final: 0.7455 (tttp) REVERT: C 338 LYS cc_start: 0.8157 (tttm) cc_final: 0.7883 (tttm) REVERT: C 381 ASP cc_start: 0.7812 (t70) cc_final: 0.7297 (t70) REVERT: D 61 MET cc_start: 0.7551 (ppp) cc_final: 0.7223 (ppp) REVERT: D 65 THR cc_start: 0.8464 (p) cc_final: 0.8173 (p) REVERT: D 111 TYR cc_start: 0.8134 (m-80) cc_final: 0.7841 (m-80) REVERT: D 118 ASP cc_start: 0.7151 (p0) cc_final: 0.6928 (p0) REVERT: D 121 CYS cc_start: 0.7662 (t) cc_final: 0.7390 (t) REVERT: D 143 THR cc_start: 0.7964 (p) cc_final: 0.7698 (t) REVERT: D 148 CYS cc_start: 0.7905 (t) cc_final: 0.7595 (t) REVERT: D 163 ASP cc_start: 0.7122 (p0) cc_final: 0.6779 (p0) REVERT: D 188 MET cc_start: 0.7196 (mmm) cc_final: 0.6632 (mmm) REVERT: D 198 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7595 (mt) REVERT: D 204 CYS cc_start: 0.7587 (m) cc_final: 0.7164 (m) REVERT: D 234 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.6666 (t80) REVERT: D 277 SER cc_start: 0.7703 (t) cc_final: 0.7428 (t) REVERT: D 284 LEU cc_start: 0.7955 (tp) cc_final: 0.7432 (tp) REVERT: N 106 MET cc_start: 0.6861 (mmm) cc_final: 0.6629 (tpp) outliers start: 26 outliers final: 20 residues processed: 241 average time/residue: 0.2689 time to fit residues: 83.4463 Evaluate side-chains 251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123902 restraints weight = 13234.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127841 restraints weight = 6702.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130457 restraints weight = 4131.353| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8676 Z= 0.252 Angle : 0.657 16.104 11797 Z= 0.336 Chirality : 0.044 0.172 1330 Planarity : 0.004 0.056 1509 Dihedral : 4.407 26.434 1201 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 2.64 % Allowed : 19.27 % Favored : 78.10 % 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: -0.53 (0.26), residues: 1096 helix: 1.55 (0.28), residues: 383 sheet: -0.71 (0.36), residues: 239 loop : -1.78 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 620 HIS 0.004 0.001 HIS D 311 PHE 0.020 0.002 PHE B 540 TYR 0.035 0.002 TYR B 498 ARG 0.009 0.000 ARG D 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3513.38 seconds wall clock time: 62 minutes 59.21 seconds (3779.21 seconds total)