Starting phenix.real_space_refine on Sun May 11 21:37:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9n_36111/05_2025/8j9n_36111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9n_36111/05_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_36111/05_2025/8j9n_36111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9n_36111/05_2025/8j9n_36111.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9n_36111/05_2025/8j9n_36111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9n_36111/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.11, per 1000 atoms: 0.72 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: 2.08 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 2.22 Time building geometry restraints manager: 2.43 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: 0.640 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- 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 8681 Z= 0.177 Angle : 0.869 24.207 11807 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 Details of bonding type rmsd hydrogen bonds : bond 0.14053 ( 357) hydrogen bonds : angle 5.95799 ( 1030) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.64360 ( 10) covalent geometry : bond 0.00384 ( 8676) covalent geometry : angle 0.86874 (11797) *********************** 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 : 0.876 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: 0.2470 time to fit residues: 76.8560 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 : 0.922 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.145510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124521 restraints weight = 13048.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128536 restraints weight = 6452.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131171 restraints weight = 3919.105| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 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 = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8681 Z= 0.165 Angle : 0.668 19.461 11807 Z= 0.341 Chirality : 0.044 0.181 1330 Planarity : 0.005 0.066 1509 Dihedral : 4.699 24.536 1201 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.38 % Allowed : 9.75 % Favored : 88.88 % 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: 0.89 (0.28), residues: 385 sheet: -0.90 (0.35), residues: 235 loop : -2.03 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 420 HIS 0.004 0.001 HIS C 220 PHE 0.033 0.002 PHE C 212 TYR 0.025 0.002 TYR B 498 ARG 0.005 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 357) hydrogen bonds : angle 4.64926 ( 1030) SS BOND : bond 0.00347 ( 5) SS BOND : angle 0.50793 ( 10) covalent geometry : bond 0.00371 ( 8676) covalent geometry : angle 0.66840 (11797) *********************** 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 250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.7109 (ttt) cc_final: 0.6891 (ttt) REVERT: B 500 PHE cc_start: 0.7113 (t80) cc_final: 0.6863 (t80) REVERT: B 554 CYS cc_start: 0.7580 (t) cc_final: 0.7150 (t) REVERT: B 558 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6117 (mm-30) REVERT: C 212 PHE cc_start: 0.6934 (p90) cc_final: 0.6649 (p90) REVERT: C 221 MET cc_start: 0.7355 (ttm) cc_final: 0.7099 (ttm) REVERT: C 274 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7505 (ttpt) REVERT: C 295 ASP cc_start: 0.7602 (m-30) cc_final: 0.7134 (m-30) REVERT: C 381 ASP cc_start: 0.7837 (t70) cc_final: 0.7244 (t0) REVERT: C 382 THR cc_start: 0.8106 (m) cc_final: 0.7901 (m) REVERT: D 65 THR cc_start: 0.8371 (p) cc_final: 0.8148 (p) REVERT: D 118 ASP cc_start: 0.7261 (p0) cc_final: 0.7027 (p0) REVERT: D 121 CYS cc_start: 0.7709 (t) cc_final: 0.7315 (t) REVERT: D 143 THR cc_start: 0.8053 (p) cc_final: 0.7775 (t) REVERT: D 148 CYS cc_start: 0.7939 (t) cc_final: 0.7546 (t) REVERT: D 177 THR cc_start: 0.8185 (m) cc_final: 0.7971 (t) REVERT: D 188 MET cc_start: 0.7342 (mmm) cc_final: 0.6847 (mmm) REVERT: D 204 CYS cc_start: 0.7625 (m) cc_final: 0.7231 (m) REVERT: D 277 SER cc_start: 0.7705 (t) cc_final: 0.7474 (t) REVERT: D 284 LEU cc_start: 0.7905 (tp) cc_final: 0.7543 (tp) REVERT: D 298 ASP cc_start: 0.8043 (t70) cc_final: 0.7783 (t0) outliers start: 12 outliers final: 6 residues processed: 241 average time/residue: 0.2514 time to fit residues: 79.1827 Evaluate side-chains 239 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 233 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 314 GLU 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: 0.1980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.144134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122961 restraints weight = 13162.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126943 restraints weight = 6539.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129573 restraints weight = 4005.554| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8681 Z= 0.180 Angle : 0.644 19.204 11807 Z= 0.330 Chirality : 0.044 0.194 1330 Planarity : 0.005 0.058 1509 Dihedral : 4.630 21.362 1201 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.41 % Allowed : 14.11 % Favored : 83.49 % 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: -0.94 (0.26), residues: 1096 helix: 1.09 (0.28), residues: 386 sheet: -0.71 (0.37), residues: 218 loop : -2.04 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.025 0.002 PHE B 540 TYR 0.021 0.002 TYR B 498 ARG 0.005 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 357) hydrogen bonds : angle 4.50143 ( 1030) SS BOND : bond 0.00391 ( 5) SS BOND : angle 0.54260 ( 10) covalent geometry : bond 0.00407 ( 8676) covalent geometry : angle 0.64456 (11797) *********************** 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 253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6721 (mmt) cc_final: 0.6212 (mmt) REVERT: B 500 PHE cc_start: 0.7140 (t80) cc_final: 0.6894 (t80) REVERT: B 558 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6128 (mm-30) REVERT: C 212 PHE cc_start: 0.6999 (p90) cc_final: 0.6689 (p90) REVERT: C 221 MET cc_start: 0.7437 (ttm) cc_final: 0.7028 (ttm) REVERT: C 274 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7552 (ttpt) REVERT: C 295 ASP cc_start: 0.7629 (m-30) cc_final: 0.7143 (m-30) REVERT: C 381 ASP cc_start: 0.7850 (t70) cc_final: 0.7217 (t0) REVERT: D 65 THR cc_start: 0.8470 (p) cc_final: 0.8217 (p) REVERT: D 118 ASP cc_start: 0.7256 (p0) cc_final: 0.6977 (p0) REVERT: D 121 CYS cc_start: 0.7655 (t) cc_final: 0.7291 (t) REVERT: D 137 ARG cc_start: 0.7107 (tpp-160) cc_final: 0.6665 (tpp-160) REVERT: D 143 THR cc_start: 0.8115 (p) cc_final: 0.7775 (t) REVERT: D 148 CYS cc_start: 0.7943 (t) cc_final: 0.7530 (t) REVERT: D 188 MET cc_start: 0.7367 (mmm) cc_final: 0.6885 (mmm) REVERT: D 204 CYS cc_start: 0.7721 (m) cc_final: 0.7284 (m) REVERT: D 277 SER cc_start: 0.7730 (t) cc_final: 0.7470 (t) REVERT: D 284 LEU cc_start: 0.8004 (tp) cc_final: 0.7598 (tp) REVERT: D 301 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7756 (mtmm) REVERT: E 45 MET cc_start: 0.5231 (tmm) cc_final: 0.4947 (tmm) outliers start: 21 outliers final: 17 residues processed: 237 average time/residue: 0.2528 time to fit residues: 77.3965 Evaluate side-chains 248 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 608 LEU 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 268 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR 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: 1.9990 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123539 restraints weight = 13187.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127615 restraints weight = 6562.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130291 restraints weight = 3987.732| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 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 = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8681 Z= 0.146 Angle : 0.631 19.043 11807 Z= 0.317 Chirality : 0.043 0.186 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.499 20.914 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.87 % Allowed : 15.14 % Favored : 82.00 % 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: -0.87 (0.26), residues: 1096 helix: 1.18 (0.28), residues: 385 sheet: -0.75 (0.36), residues: 220 loop : -1.97 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.035 0.002 PHE B 540 TYR 0.022 0.002 TYR B 498 ARG 0.008 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 357) hydrogen bonds : angle 4.37171 ( 1030) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.48968 ( 10) covalent geometry : bond 0.00332 ( 8676) covalent geometry : angle 0.63073 (11797) *********************** 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 : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6795 (mmt) cc_final: 0.6277 (mmt) REVERT: B 408 MET cc_start: 0.7428 (ttt) cc_final: 0.7118 (ttp) REVERT: B 496 PHE cc_start: 0.7570 (t80) cc_final: 0.7246 (t80) REVERT: B 500 PHE cc_start: 0.7143 (t80) cc_final: 0.6928 (t80) REVERT: B 540 PHE cc_start: 0.7589 (t80) cc_final: 0.7369 (t80) REVERT: B 558 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6113 (mm-30) REVERT: C 15 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: C 212 PHE cc_start: 0.6973 (p90) cc_final: 0.6693 (p90) REVERT: C 274 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7559 (ttpt) REVERT: C 336 ARG cc_start: 0.6455 (ttt-90) cc_final: 0.6069 (mtp85) REVERT: C 381 ASP cc_start: 0.7844 (t70) cc_final: 0.7123 (t0) REVERT: D 17 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8342 (tm-30) REVERT: D 65 THR cc_start: 0.8498 (p) cc_final: 0.8245 (p) REVERT: D 118 ASP cc_start: 0.7206 (p0) cc_final: 0.6935 (p0) REVERT: D 121 CYS cc_start: 0.7639 (t) cc_final: 0.7300 (t) REVERT: D 137 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6669 (tpp-160) REVERT: D 143 THR cc_start: 0.8109 (p) cc_final: 0.7781 (t) REVERT: D 148 CYS cc_start: 0.7906 (t) cc_final: 0.7517 (t) REVERT: D 150 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8195 (mmt-90) REVERT: D 188 MET cc_start: 0.7346 (mmm) cc_final: 0.6881 (mmm) REVERT: D 204 CYS cc_start: 0.7688 (m) cc_final: 0.7248 (m) REVERT: D 277 SER cc_start: 0.7733 (t) cc_final: 0.7476 (t) REVERT: D 284 LEU cc_start: 0.7967 (tp) cc_final: 0.7522 (tp) REVERT: D 301 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7710 (mtmm) REVERT: E 45 MET cc_start: 0.5159 (tmm) cc_final: 0.4936 (tmm) outliers start: 25 outliers final: 20 residues processed: 240 average time/residue: 0.2516 time to fit residues: 77.7550 Evaluate side-chains 255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 268 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 317 ARG 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 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: 0.3980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125022 restraints weight = 12977.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128915 restraints weight = 6577.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131575 restraints weight = 4064.035| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 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 = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8681 Z= 0.128 Angle : 0.622 18.985 11807 Z= 0.311 Chirality : 0.042 0.169 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.401 20.557 1201 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.10 % Allowed : 14.22 % Favored : 82.68 % 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: -0.81 (0.26), residues: 1096 helix: 1.27 (0.28), residues: 383 sheet: -0.75 (0.36), residues: 220 loop : -1.95 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 420 HIS 0.003 0.001 HIS C 220 PHE 0.033 0.001 PHE B 540 TYR 0.027 0.002 TYR B 607 ARG 0.004 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 357) hydrogen bonds : angle 4.20887 ( 1030) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.45605 ( 10) covalent geometry : bond 0.00292 ( 8676) covalent geometry : angle 0.62240 (11797) *********************** 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 : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6604 (mmt) cc_final: 0.6139 (mmt) REVERT: B 496 PHE cc_start: 0.7531 (t80) cc_final: 0.7250 (t80) REVERT: B 558 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6023 (mm-30) REVERT: C 15 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6421 (tp30) REVERT: C 212 PHE cc_start: 0.6972 (p90) cc_final: 0.6751 (p90) REVERT: C 221 MET cc_start: 0.7330 (ttm) cc_final: 0.7045 (ttp) REVERT: C 274 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7593 (ttpt) REVERT: C 295 ASP cc_start: 0.7630 (m-30) cc_final: 0.7011 (m-30) REVERT: C 381 ASP cc_start: 0.7802 (t70) cc_final: 0.7020 (t0) REVERT: C 385 GLN cc_start: 0.8132 (tp40) cc_final: 0.7830 (mm-40) REVERT: D 17 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 65 THR cc_start: 0.8509 (p) cc_final: 0.8248 (p) REVERT: D 111 TYR cc_start: 0.8152 (m-80) cc_final: 0.7865 (m-80) REVERT: D 118 ASP cc_start: 0.7165 (p0) cc_final: 0.6891 (p0) REVERT: D 121 CYS cc_start: 0.7498 (t) cc_final: 0.7219 (t) REVERT: D 137 ARG cc_start: 0.7060 (tpp-160) cc_final: 0.6665 (tpp-160) REVERT: D 143 THR cc_start: 0.8097 (p) cc_final: 0.7591 (t) REVERT: D 148 CYS cc_start: 0.7869 (t) cc_final: 0.7480 (t) REVERT: D 188 MET cc_start: 0.7204 (mmm) cc_final: 0.6666 (mmm) REVERT: D 204 CYS cc_start: 0.7571 (m) cc_final: 0.7186 (m) REVERT: D 234 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7343 (t80) REVERT: D 277 SER cc_start: 0.7640 (t) cc_final: 0.7396 (t) REVERT: D 284 LEU cc_start: 0.7949 (tp) cc_final: 0.7532 (tp) outliers start: 27 outliers final: 20 residues processed: 248 average time/residue: 0.2490 time to fit residues: 79.9451 Evaluate side-chains 259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 608 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 259 GLN 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: 4.9990 chunk 94 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.144987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124098 restraints weight = 13000.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128023 restraints weight = 6618.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130599 restraints weight = 4096.895| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- 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: 0.7065 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8681 Z= 0.157 Angle : 0.643 19.879 11807 Z= 0.323 Chirality : 0.043 0.170 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.453 24.730 1201 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.98 % Allowed : 15.02 % Favored : 82.00 % 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: 1.39 (0.28), residues: 383 sheet: -0.73 (0.37), residues: 212 loop : -1.94 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 427 HIS 0.004 0.001 HIS D 183 PHE 0.037 0.002 PHE B 540 TYR 0.019 0.002 TYR B 498 ARG 0.005 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 357) hydrogen bonds : angle 4.22474 ( 1030) SS BOND : bond 0.00318 ( 5) SS BOND : angle 0.51293 ( 10) covalent geometry : bond 0.00356 ( 8676) covalent geometry : angle 0.64264 (11797) *********************** 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: 26 poor density : 232 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6536 (mmt) cc_final: 0.6060 (mmt) REVERT: B 496 PHE cc_start: 0.7532 (t80) cc_final: 0.7262 (t80) REVERT: B 558 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6028 (mm-30) REVERT: C 15 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: C 30 ARG cc_start: 0.7798 (tpp80) cc_final: 0.7339 (tpp80) REVERT: C 221 MET cc_start: 0.7318 (ttm) cc_final: 0.7038 (ttp) REVERT: C 274 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7605 (ttpt) REVERT: C 295 ASP cc_start: 0.7634 (m-30) cc_final: 0.7227 (m-30) REVERT: C 381 ASP cc_start: 0.7814 (t70) cc_final: 0.7054 (t0) REVERT: D 17 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 65 THR cc_start: 0.8543 (p) cc_final: 0.8285 (p) REVERT: D 111 TYR cc_start: 0.8159 (m-80) cc_final: 0.7893 (m-80) REVERT: D 118 ASP cc_start: 0.7166 (p0) cc_final: 0.6922 (p0) REVERT: D 121 CYS cc_start: 0.7605 (t) cc_final: 0.7400 (t) REVERT: D 137 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6754 (tpp-160) REVERT: D 143 THR cc_start: 0.7978 (p) cc_final: 0.7759 (t) REVERT: D 148 CYS cc_start: 0.7895 (t) cc_final: 0.7539 (t) REVERT: D 163 ASP cc_start: 0.7358 (p0) cc_final: 0.6891 (p0) REVERT: D 188 MET cc_start: 0.7202 (mmm) cc_final: 0.6686 (mmm) REVERT: D 204 CYS cc_start: 0.7597 (m) cc_final: 0.7201 (m) REVERT: D 234 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7109 (t80) REVERT: D 277 SER cc_start: 0.7633 (t) cc_final: 0.7373 (t) REVERT: D 284 LEU cc_start: 0.7958 (tp) cc_final: 0.7531 (tp) REVERT: D 301 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7693 (mtmm) outliers start: 26 outliers final: 23 residues processed: 238 average time/residue: 0.2513 time to fit residues: 77.5555 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 268 GLU Chi-restraints excluded: chain C residue 317 ARG 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 234 PHE 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: 2.9990 chunk 79 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.144832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123093 restraints weight = 13021.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127278 restraints weight = 6438.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129967 restraints weight = 3907.464| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 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 = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8681 Z= 0.160 Angle : 0.655 19.842 11807 Z= 0.328 Chirality : 0.043 0.159 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.486 24.037 1201 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.10 % Allowed : 16.51 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1096 helix: 1.44 (0.28), residues: 384 sheet: -0.71 (0.38), residues: 214 loop : -1.91 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.040 0.002 PHE B 540 TYR 0.021 0.002 TYR B 498 ARG 0.010 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 357) hydrogen bonds : angle 4.21730 ( 1030) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.50287 ( 10) covalent geometry : bond 0.00362 ( 8676) covalent geometry : angle 0.65558 (11797) *********************** 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 260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6654 (mmt) cc_final: 0.6122 (mmt) REVERT: B 496 PHE cc_start: 0.7548 (t80) cc_final: 0.7304 (t80) REVERT: B 558 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6071 (mm-30) REVERT: C 15 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: C 30 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7341 (tpp80) REVERT: C 221 MET cc_start: 0.7370 (ttm) cc_final: 0.7045 (ttp) REVERT: C 274 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7597 (ttpt) REVERT: C 295 ASP cc_start: 0.7741 (m-30) cc_final: 0.6951 (m-30) REVERT: C 381 ASP cc_start: 0.7837 (t70) cc_final: 0.7041 (t0) REVERT: D 65 THR cc_start: 0.8556 (p) cc_final: 0.8306 (p) REVERT: D 111 TYR cc_start: 0.8169 (m-80) cc_final: 0.7905 (m-80) REVERT: D 118 ASP cc_start: 0.7159 (p0) cc_final: 0.6910 (p0) REVERT: D 121 CYS cc_start: 0.7681 (t) cc_final: 0.7465 (t) REVERT: D 137 ARG cc_start: 0.7149 (tpp-160) cc_final: 0.6833 (tpp-160) REVERT: D 143 THR cc_start: 0.8012 (p) cc_final: 0.7743 (t) REVERT: D 148 CYS cc_start: 0.7891 (t) cc_final: 0.7527 (t) REVERT: D 163 ASP cc_start: 0.7318 (p0) cc_final: 0.7095 (p0) REVERT: D 188 MET cc_start: 0.7270 (mmm) cc_final: 0.6819 (mmm) REVERT: D 198 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7681 (mt) REVERT: D 204 CYS cc_start: 0.7674 (m) cc_final: 0.7250 (m) REVERT: D 234 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6999 (t80) REVERT: D 277 SER cc_start: 0.7687 (t) cc_final: 0.7406 (t) REVERT: D 284 LEU cc_start: 0.7962 (tp) cc_final: 0.7751 (tp) REVERT: D 301 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7654 (mtmm) outliers start: 27 outliers final: 23 residues processed: 240 average time/residue: 0.2523 time to fit residues: 79.2228 Evaluate side-chains 256 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 268 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 C residue 393 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 234 PHE 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: 3.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS C 19 GLN D 88 ASN D 237 ASN D 259 GLN N 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123123 restraints weight = 13235.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127065 restraints weight = 6736.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129673 restraints weight = 4174.534| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8681 Z= 0.187 Angle : 0.676 20.328 11807 Z= 0.341 Chirality : 0.044 0.162 1330 Planarity : 0.005 0.056 1509 Dihedral : 4.566 25.098 1201 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.56 % Allowed : 16.63 % Favored : 79.82 % 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: -0.75 (0.26), residues: 1096 helix: 1.34 (0.28), residues: 385 sheet: -0.66 (0.37), residues: 219 loop : -1.97 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 427 HIS 0.005 0.001 HIS D 183 PHE 0.028 0.002 PHE B 540 TYR 0.022 0.002 TYR B 498 ARG 0.009 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 357) hydrogen bonds : angle 4.28786 ( 1030) SS BOND : bond 0.00396 ( 5) SS BOND : angle 0.54081 ( 10) covalent geometry : bond 0.00420 ( 8676) covalent geometry : angle 0.67576 (11797) *********************** 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 266 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 GLU cc_start: 0.7030 (tp30) cc_final: 0.6563 (tp30) REVERT: B 407 MET cc_start: 0.6613 (mmt) cc_final: 0.6138 (mmt) REVERT: B 496 PHE cc_start: 0.7504 (t80) cc_final: 0.7269 (t80) REVERT: B 558 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6069 (mm-30) REVERT: B 600 PHE cc_start: 0.6099 (t80) cc_final: 0.5437 (m-80) REVERT: C 15 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: C 29 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7342 (tt) REVERT: C 30 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7298 (tpp80) REVERT: C 221 MET cc_start: 0.7309 (ttm) cc_final: 0.7056 (ttp) REVERT: C 274 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7612 (ttpt) REVERT: C 295 ASP cc_start: 0.7537 (m-30) cc_final: 0.6860 (m-30) REVERT: C 381 ASP cc_start: 0.7836 (t70) cc_final: 0.7064 (t0) REVERT: D 17 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 65 THR cc_start: 0.8570 (p) cc_final: 0.8313 (p) REVERT: D 118 ASP cc_start: 0.7092 (p0) cc_final: 0.6842 (p0) REVERT: D 137 ARG cc_start: 0.7108 (tpp-160) cc_final: 0.6850 (tpp-160) REVERT: D 143 THR cc_start: 0.8014 (p) cc_final: 0.7720 (t) REVERT: D 148 CYS cc_start: 0.7873 (t) cc_final: 0.7532 (t) REVERT: D 163 ASP cc_start: 0.7309 (p0) cc_final: 0.7065 (p0) REVERT: D 188 MET cc_start: 0.7175 (mmm) cc_final: 0.6751 (mmm) REVERT: D 198 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7680 (mt) REVERT: D 204 CYS cc_start: 0.7612 (m) cc_final: 0.7212 (m) REVERT: D 234 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7012 (t80) REVERT: D 277 SER cc_start: 0.7627 (t) cc_final: 0.7363 (t) REVERT: D 284 LEU cc_start: 0.7958 (tp) cc_final: 0.7745 (tp) REVERT: D 304 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7901 (ptm160) outliers start: 31 outliers final: 25 residues processed: 244 average time/residue: 0.2665 time to fit residues: 84.7245 Evaluate side-chains 259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 268 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 314 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 C residue 393 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS D 237 ASN D 259 GLN N 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123926 restraints weight = 13032.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127880 restraints weight = 6609.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130497 restraints weight = 4050.274| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 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 = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8681 Z= 0.163 Angle : 0.680 20.873 11807 Z= 0.340 Chirality : 0.044 0.168 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.569 27.679 1201 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.56 % Allowed : 17.32 % Favored : 79.13 % 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: -0.76 (0.26), residues: 1096 helix: 1.34 (0.28), residues: 385 sheet: -0.70 (0.37), residues: 229 loop : -1.98 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.031 0.002 PHE B 540 TYR 0.025 0.002 TYR B 498 ARG 0.010 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 357) hydrogen bonds : angle 4.27025 ( 1030) SS BOND : bond 0.00342 ( 5) SS BOND : angle 0.51380 ( 10) covalent geometry : bond 0.00368 ( 8676) covalent geometry : angle 0.67989 (11797) *********************** 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 263 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 GLU cc_start: 0.7025 (tp30) cc_final: 0.6787 (tp30) REVERT: B 352 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 407 MET cc_start: 0.6594 (mmt) cc_final: 0.6127 (mmt) REVERT: B 496 PHE cc_start: 0.7555 (t80) cc_final: 0.7319 (t80) REVERT: B 558 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6059 (mm-30) REVERT: C 29 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7317 (tt) REVERT: C 30 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7316 (tpp80) REVERT: C 221 MET cc_start: 0.7321 (ttm) cc_final: 0.7052 (ttp) REVERT: C 274 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7609 (ttpt) REVERT: C 295 ASP cc_start: 0.7559 (m-30) cc_final: 0.6889 (m-30) REVERT: C 381 ASP cc_start: 0.7830 (t70) cc_final: 0.7056 (t0) REVERT: D 17 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 65 THR cc_start: 0.8586 (p) cc_final: 0.8329 (p) REVERT: D 118 ASP cc_start: 0.7062 (p0) cc_final: 0.6764 (p0) REVERT: D 143 THR cc_start: 0.8004 (p) cc_final: 0.7574 (t) REVERT: D 148 CYS cc_start: 0.7881 (t) cc_final: 0.7520 (t) REVERT: D 188 MET cc_start: 0.7165 (mmm) cc_final: 0.6772 (mmm) REVERT: D 198 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7657 (mt) REVERT: D 204 CYS cc_start: 0.7601 (m) cc_final: 0.7205 (m) REVERT: D 234 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6932 (t80) REVERT: D 277 SER cc_start: 0.7642 (t) cc_final: 0.7385 (t) REVERT: D 304 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7899 (ptm160) outliers start: 31 outliers final: 25 residues processed: 242 average time/residue: 0.2469 time to fit residues: 77.9847 Evaluate side-chains 260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 B residue 608 LEU 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 268 GLU Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 314 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 C residue 393 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** C 387 ASN D 88 ASN D 237 ASN D 259 GLN N 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124016 restraints weight = 13040.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127932 restraints weight = 6664.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130638 restraints weight = 4136.742| |-----------------------------------------------------------------------------| 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: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8681 Z= 0.152 Angle : 0.675 21.532 11807 Z= 0.336 Chirality : 0.043 0.161 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.558 30.520 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.44 % Allowed : 17.66 % Favored : 78.90 % 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: -0.71 (0.26), residues: 1096 helix: 1.37 (0.28), residues: 382 sheet: -0.69 (0.37), residues: 229 loop : -1.91 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 PHE 0.029 0.002 PHE B 540 TYR 0.025 0.002 TYR B 498 ARG 0.010 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 357) hydrogen bonds : angle 4.25877 ( 1030) SS BOND : bond 0.00312 ( 5) SS BOND : angle 0.47384 ( 10) covalent geometry : bond 0.00345 ( 8676) covalent geometry : angle 0.67487 (11797) ********************** 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 265 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 407 MET cc_start: 0.6564 (mmt) cc_final: 0.6104 (mmt) REVERT: B 558 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6041 (mm-30) REVERT: C 29 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7284 (tt) REVERT: C 30 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7333 (tpp80) REVERT: C 221 MET cc_start: 0.7308 (ttm) cc_final: 0.7048 (ttp) REVERT: C 274 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7600 (ttpt) REVERT: C 295 ASP cc_start: 0.7557 (m-30) cc_final: 0.6882 (m-30) REVERT: C 381 ASP cc_start: 0.7825 (t70) cc_final: 0.7052 (t0) REVERT: D 17 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 61 MET cc_start: 0.7426 (ppp) cc_final: 0.6930 (ppp) REVERT: D 65 THR cc_start: 0.8589 (p) cc_final: 0.8327 (p) REVERT: D 111 TYR cc_start: 0.8162 (m-80) cc_final: 0.7917 (m-80) REVERT: D 118 ASP cc_start: 0.7033 (p0) cc_final: 0.6742 (p0) REVERT: D 143 THR cc_start: 0.7940 (p) cc_final: 0.7699 (t) REVERT: D 148 CYS cc_start: 0.7892 (t) cc_final: 0.7491 (t) REVERT: D 163 ASP cc_start: 0.7235 (p0) cc_final: 0.6870 (p0) REVERT: D 188 MET cc_start: 0.7143 (mmm) cc_final: 0.6739 (mmm) REVERT: D 198 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7682 (mt) REVERT: D 204 CYS cc_start: 0.7578 (m) cc_final: 0.7182 (m) REVERT: D 234 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.6920 (t80) REVERT: D 277 SER cc_start: 0.7648 (t) cc_final: 0.7395 (t) REVERT: D 304 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7909 (ptm160) outliers start: 30 outliers final: 22 residues processed: 242 average time/residue: 0.2419 time to fit residues: 76.2523 Evaluate side-chains 257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 314 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 C residue 393 LEU Chi-restraints excluded: chain D residue 198 LEU 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 13 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** C 387 ASN D 237 ASN D 259 GLN N 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124816 restraints weight = 13092.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128792 restraints weight = 6608.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131294 restraints weight = 4045.350| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 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 = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8681 Z= 0.144 Angle : 0.656 14.864 11807 Z= 0.330 Chirality : 0.043 0.159 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.564 35.307 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.21 % Allowed : 18.35 % Favored : 78.44 % 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: -0.70 (0.26), residues: 1096 helix: 1.36 (0.28), residues: 383 sheet: -0.67 (0.37), residues: 229 loop : -1.90 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 PHE 0.029 0.002 PHE B 540 TYR 0.025 0.001 TYR B 498 ARG 0.009 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 357) hydrogen bonds : angle 4.18595 ( 1030) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.46485 ( 10) covalent geometry : bond 0.00328 ( 8676) covalent geometry : angle 0.65648 (11797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.10 seconds wall clock time: 59 minutes 10.18 seconds (3550.18 seconds total)