Starting phenix.real_space_refine on Fri Aug 22 23:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9n_36111/08_2025/8j9n_36111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9n_36111/08_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_36111/08_2025/8j9n_36111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9n_36111/08_2025/8j9n_36111.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9n_36111/08_2025/8j9n_36111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9n_36111/08_2025/8j9n_36111.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1} 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: {'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'GLU: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: {'ASP:plan': 2, 'ARG:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1} 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, 'ARG:plan': 1, 'GLU:plan': 4} 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: 1.91, per 1000 atoms: 0.23 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: 0.58 Conformation dependent library (CDL) restraints added in 312.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 0.85 Time building geometry restraints manager: 0.75 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: 0.900 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG D 251 TYR 0.035 0.002 TYR B 498 PHE 0.035 0.002 PHE B 600 TRP 0.019 0.002 TRP D 63 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8676) covalent geometry : angle 0.86874 (11797) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.64360 ( 10) hydrogen bonds : bond 0.14053 ( 357) hydrogen bonds : angle 5.95799 ( 1030) *********************** 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 : 0.273 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: 0.0880 time to fit residues: 28.1312 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 : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.144636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123658 restraints weight = 13112.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127684 restraints weight = 6475.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130265 restraints weight = 3923.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132105 restraints weight = 2738.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133291 restraints weight = 2074.318| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1151 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= 0.179 Angle : 0.674 18.824 11807 Z= 0.345 Chirality : 0.044 0.191 1330 Planarity : 0.005 0.065 1509 Dihedral : 4.735 23.882 1201 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.38 % Allowed : 9.63 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.25), residues: 1096 helix: 0.86 (0.28), residues: 385 sheet: -0.89 (0.36), residues: 225 loop : -2.00 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 49 TYR 0.025 0.002 TYR B 498 PHE 0.032 0.002 PHE C 212 TRP 0.020 0.002 TRP B 420 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8676) covalent geometry : angle 0.67448 (11797) SS BOND : bond 0.00407 ( 5) SS BOND : angle 0.52465 ( 10) hydrogen bonds : bond 0.04175 ( 357) hydrogen bonds : angle 4.66235 ( 1030) *********************** 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 : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.7114 (ttt) cc_final: 0.6897 (ttt) REVERT: B 500 PHE cc_start: 0.7144 (t80) cc_final: 0.6870 (t80) REVERT: B 505 PHE cc_start: 0.7820 (m-10) cc_final: 0.7606 (m-10) REVERT: B 558 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6157 (mm-30) REVERT: C 212 PHE cc_start: 0.6921 (p90) cc_final: 0.6638 (p90) REVERT: C 221 MET cc_start: 0.7388 (ttm) cc_final: 0.7165 (ttm) REVERT: C 274 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7514 (ttpt) REVERT: C 295 ASP cc_start: 0.7577 (m-30) cc_final: 0.7103 (m-30) REVERT: C 381 ASP cc_start: 0.7851 (t70) cc_final: 0.7266 (t0) REVERT: C 382 THR cc_start: 0.8091 (m) cc_final: 0.7881 (m) REVERT: D 65 THR cc_start: 0.8381 (p) cc_final: 0.8152 (p) REVERT: D 111 TYR cc_start: 0.8208 (m-80) cc_final: 0.7893 (m-80) REVERT: D 118 ASP cc_start: 0.7249 (p0) cc_final: 0.6981 (p0) REVERT: D 121 CYS cc_start: 0.7709 (t) cc_final: 0.7324 (t) REVERT: D 143 THR cc_start: 0.8056 (p) cc_final: 0.7767 (t) REVERT: D 148 CYS cc_start: 0.7931 (t) cc_final: 0.7558 (t) REVERT: D 156 GLN cc_start: 0.6880 (mt0) cc_final: 0.6671 (mt0) REVERT: D 177 THR cc_start: 0.8210 (m) cc_final: 0.7992 (t) REVERT: D 188 MET cc_start: 0.7375 (mmm) cc_final: 0.6905 (mmm) REVERT: D 204 CYS cc_start: 0.7687 (m) cc_final: 0.7269 (m) REVERT: D 277 SER cc_start: 0.7732 (t) cc_final: 0.7479 (t) REVERT: D 284 LEU cc_start: 0.7940 (tp) cc_final: 0.7730 (tt) REVERT: D 298 ASP cc_start: 0.8051 (t70) cc_final: 0.7758 (t0) outliers start: 12 outliers final: 9 residues processed: 242 average time/residue: 0.0869 time to fit residues: 27.3876 Evaluate side-chains 244 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 259 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123609 restraints weight = 13026.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127594 restraints weight = 6462.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130248 restraints weight = 3929.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132065 restraints weight = 2731.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133291 restraints weight = 2070.163| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8681 Z= 0.168 Angle : 0.634 19.009 11807 Z= 0.326 Chirality : 0.044 0.207 1330 Planarity : 0.005 0.058 1509 Dihedral : 4.613 21.249 1201 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.52 % Allowed : 13.19 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.26), residues: 1096 helix: 1.07 (0.28), residues: 386 sheet: -0.74 (0.37), residues: 213 loop : -1.98 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.026 0.002 TYR B 544 PHE 0.035 0.002 PHE B 540 TRP 0.048 0.002 TRP B 420 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8676) covalent geometry : angle 0.63376 (11797) SS BOND : bond 0.00352 ( 5) SS BOND : angle 0.51794 ( 10) hydrogen bonds : bond 0.03930 ( 357) hydrogen bonds : angle 4.48189 ( 1030) *********************** 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 256 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6700 (mmt) cc_final: 0.6192 (mmt) REVERT: B 496 PHE cc_start: 0.7595 (t80) cc_final: 0.7244 (t80) REVERT: B 500 PHE cc_start: 0.7170 (t80) cc_final: 0.6896 (t80) REVERT: B 558 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6127 (mm-30) REVERT: C 30 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7387 (tpp80) REVERT: C 212 PHE cc_start: 0.6985 (p90) cc_final: 0.6665 (p90) REVERT: C 221 MET cc_start: 0.7433 (ttm) cc_final: 0.7060 (ttm) REVERT: C 274 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7530 (ttpt) REVERT: C 295 ASP cc_start: 0.7583 (m-30) cc_final: 0.7101 (m-30) REVERT: C 300 LYS cc_start: 0.8256 (tttm) cc_final: 0.7988 (tttp) REVERT: C 336 ARG cc_start: 0.6361 (ttp80) cc_final: 0.6112 (mtp85) REVERT: C 381 ASP cc_start: 0.7857 (t70) cc_final: 0.7216 (t0) REVERT: C 382 THR cc_start: 0.8078 (m) cc_final: 0.7863 (m) REVERT: D 65 THR cc_start: 0.8478 (p) cc_final: 0.8225 (p) REVERT: D 118 ASP cc_start: 0.7217 (p0) cc_final: 0.6951 (p0) REVERT: D 121 CYS cc_start: 0.7634 (t) cc_final: 0.7279 (t) REVERT: D 143 THR cc_start: 0.8110 (p) cc_final: 0.7771 (t) REVERT: D 148 CYS cc_start: 0.7894 (t) cc_final: 0.7504 (t) REVERT: D 188 MET cc_start: 0.7365 (mmm) cc_final: 0.6903 (mmm) REVERT: D 204 CYS cc_start: 0.7691 (m) cc_final: 0.7264 (m) REVERT: D 277 SER cc_start: 0.7736 (t) cc_final: 0.7476 (t) REVERT: D 284 LEU cc_start: 0.7987 (tp) cc_final: 0.7561 (tp) REVERT: D 304 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7783 (ptm160) REVERT: E 45 MET cc_start: 0.5192 (tmm) cc_final: 0.4942 (tmm) outliers start: 22 outliers final: 17 residues processed: 240 average time/residue: 0.0843 time to fit residues: 26.3834 Evaluate side-chains 250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 201 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.145428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124087 restraints weight = 13256.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128124 restraints weight = 6559.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130902 restraints weight = 4002.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132663 restraints weight = 2760.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133943 restraints weight = 2103.664| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1619 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= 0.137 Angle : 0.627 19.890 11807 Z= 0.314 Chirality : 0.043 0.205 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.473 20.855 1201 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.75 % Allowed : 14.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.26), residues: 1096 helix: 1.17 (0.28), residues: 385 sheet: -0.67 (0.37), residues: 218 loop : -1.98 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 49 TYR 0.025 0.002 TYR B 544 PHE 0.034 0.002 PHE B 540 TRP 0.042 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8676) covalent geometry : angle 0.62693 (11797) SS BOND : bond 0.00277 ( 5) SS BOND : angle 0.47232 ( 10) hydrogen bonds : bond 0.03656 ( 357) hydrogen bonds : angle 4.30425 ( 1030) *********************** 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: 24 poor density : 236 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6670 (mmt) cc_final: 0.6171 (mmt) REVERT: B 408 MET cc_start: 0.7430 (ttt) cc_final: 0.7188 (ttp) REVERT: B 496 PHE cc_start: 0.7556 (t80) cc_final: 0.7211 (t80) REVERT: B 500 PHE cc_start: 0.7207 (t80) cc_final: 0.6933 (t80) REVERT: B 505 PHE cc_start: 0.7740 (m-10) cc_final: 0.7492 (m-10) REVERT: B 558 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6098 (mm-30) REVERT: C 212 PHE cc_start: 0.6949 (p90) cc_final: 0.6649 (p90) REVERT: C 274 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7549 (ttpt) REVERT: C 336 ARG cc_start: 0.6344 (ttp80) cc_final: 0.6132 (mtp85) REVERT: C 338 LYS cc_start: 0.8257 (tttm) cc_final: 0.7901 (tttm) REVERT: C 381 ASP cc_start: 0.7848 (t70) cc_final: 0.7166 (t0) REVERT: C 382 THR cc_start: 0.8057 (m) cc_final: 0.7837 (m) REVERT: D 17 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8324 (tm-30) REVERT: D 65 THR cc_start: 0.8454 (p) cc_final: 0.8198 (p) REVERT: D 111 TYR cc_start: 0.8159 (m-80) cc_final: 0.7875 (m-80) REVERT: D 118 ASP cc_start: 0.7169 (p0) cc_final: 0.6907 (p0) REVERT: D 121 CYS cc_start: 0.7606 (t) cc_final: 0.7279 (t) REVERT: D 137 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6670 (tpp-160) REVERT: D 143 THR cc_start: 0.8074 (p) cc_final: 0.7755 (t) REVERT: D 148 CYS cc_start: 0.7865 (t) cc_final: 0.7515 (t) REVERT: D 188 MET cc_start: 0.7331 (mmm) cc_final: 0.6880 (mmm) REVERT: D 204 CYS cc_start: 0.7663 (m) cc_final: 0.7243 (m) REVERT: D 277 SER cc_start: 0.7751 (t) cc_final: 0.7481 (t) REVERT: D 284 LEU cc_start: 0.7969 (tp) cc_final: 0.7519 (tp) outliers start: 24 outliers final: 18 residues processed: 242 average time/residue: 0.0907 time to fit residues: 28.5399 Evaluate side-chains 254 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR 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 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 101 MET 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 96 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 102 optimal weight: 0.0770 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.145813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124364 restraints weight = 13100.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128451 restraints weight = 6526.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131148 restraints weight = 3981.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132935 restraints weight = 2772.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134223 restraints weight = 2119.729| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1708 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= 0.135 Angle : 0.619 19.261 11807 Z= 0.311 Chirality : 0.042 0.164 1330 Planarity : 0.004 0.057 1509 Dihedral : 4.388 19.671 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.98 % Allowed : 14.91 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.26), residues: 1096 helix: 1.34 (0.28), residues: 383 sheet: -0.70 (0.37), residues: 218 loop : -1.94 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.017 0.001 TYR B 498 PHE 0.021 0.001 PHE C 212 TRP 0.015 0.002 TRP B 427 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8676) covalent geometry : angle 0.61900 (11797) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.44636 ( 10) hydrogen bonds : bond 0.03563 ( 357) hydrogen bonds : angle 4.20060 ( 1030) *********************** 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 265 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6801 (mm-30) REVERT: B 407 MET cc_start: 0.6644 (mmt) cc_final: 0.6157 (mmt) REVERT: B 408 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7105 (ttt) REVERT: B 496 PHE cc_start: 0.7557 (t80) cc_final: 0.7244 (t80) REVERT: B 500 PHE cc_start: 0.7140 (t80) cc_final: 0.6870 (t80) REVERT: B 549 THR cc_start: 0.7144 (t) cc_final: 0.6910 (p) REVERT: B 558 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6061 (mm-30) REVERT: C 212 PHE cc_start: 0.6980 (p90) cc_final: 0.6751 (p90) REVERT: C 221 MET cc_start: 0.7417 (ttm) cc_final: 0.7064 (ttp) REVERT: C 274 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7577 (ttpt) REVERT: C 295 ASP cc_start: 0.7717 (m-30) cc_final: 0.7057 (m-30) REVERT: C 381 ASP cc_start: 0.7846 (t70) cc_final: 0.7115 (t0) REVERT: C 382 THR cc_start: 0.8091 (m) cc_final: 0.7861 (m) REVERT: C 385 GLN cc_start: 0.8187 (tp40) cc_final: 0.7866 (mm-40) REVERT: D 17 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8363 (tm-30) REVERT: D 65 THR cc_start: 0.8478 (p) cc_final: 0.8207 (p) REVERT: D 111 TYR cc_start: 0.8155 (m-80) cc_final: 0.7868 (m-80) REVERT: D 118 ASP cc_start: 0.7168 (p0) cc_final: 0.6927 (p0) REVERT: D 121 CYS cc_start: 0.7555 (t) cc_final: 0.7246 (t) REVERT: D 137 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.6669 (tpp-160) REVERT: D 143 THR cc_start: 0.8079 (p) cc_final: 0.7742 (t) REVERT: D 148 CYS cc_start: 0.7880 (t) cc_final: 0.7484 (t) REVERT: D 188 MET cc_start: 0.7295 (mmm) cc_final: 0.6832 (mmm) REVERT: D 204 CYS cc_start: 0.7660 (m) cc_final: 0.7249 (m) REVERT: D 234 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7213 (t80) REVERT: D 277 SER cc_start: 0.7723 (t) cc_final: 0.7436 (t) REVERT: D 284 LEU cc_start: 0.7991 (tp) cc_final: 0.7538 (tp) outliers start: 26 outliers final: 21 residues processed: 246 average time/residue: 0.0849 time to fit residues: 27.1917 Evaluate side-chains 262 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 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 310 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 47 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 0.0040 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3330 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.146700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125353 restraints weight = 12959.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129348 restraints weight = 6501.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132052 restraints weight = 3999.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133877 restraints weight = 2788.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135051 restraints weight = 2136.189| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8681 Z= 0.114 Angle : 0.609 19.556 11807 Z= 0.304 Chirality : 0.042 0.156 1330 Planarity : 0.004 0.058 1509 Dihedral : 4.304 20.673 1201 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.87 % Allowed : 15.60 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1096 helix: 1.42 (0.28), residues: 383 sheet: -0.87 (0.36), residues: 232 loop : -1.86 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 49 TYR 0.019 0.001 TYR B 498 PHE 0.025 0.001 PHE B 540 TRP 0.016 0.001 TRP B 420 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8676) covalent geometry : angle 0.60942 (11797) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.41013 ( 10) hydrogen bonds : bond 0.03351 ( 357) hydrogen bonds : angle 4.13707 ( 1030) *********************** 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 261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6587 (mmt) cc_final: 0.6146 (mmt) REVERT: B 496 PHE cc_start: 0.7517 (t80) cc_final: 0.7240 (t80) REVERT: B 500 PHE cc_start: 0.7110 (t80) cc_final: 0.6848 (t80) REVERT: B 549 THR cc_start: 0.7122 (t) cc_final: 0.6836 (p) REVERT: B 558 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5958 (mm-30) REVERT: C 221 MET cc_start: 0.7373 (ttm) cc_final: 0.7040 (ttm) REVERT: C 274 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7573 (ttpt) REVERT: C 295 ASP cc_start: 0.7683 (m-30) cc_final: 0.7238 (m-30) REVERT: C 338 LYS cc_start: 0.8221 (tttm) cc_final: 0.8005 (tttm) REVERT: C 381 ASP cc_start: 0.7845 (t70) cc_final: 0.7082 (t0) REVERT: C 382 THR cc_start: 0.8083 (m) cc_final: 0.7841 (m) REVERT: C 385 GLN cc_start: 0.8179 (tp40) cc_final: 0.7874 (mm-40) REVERT: D 17 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 61 MET cc_start: 0.7691 (ppp) cc_final: 0.6803 (ppp) REVERT: D 65 THR cc_start: 0.8462 (p) cc_final: 0.8192 (p) REVERT: D 111 TYR cc_start: 0.8140 (m-80) cc_final: 0.7848 (m-80) REVERT: D 118 ASP cc_start: 0.7160 (p0) cc_final: 0.6927 (p0) REVERT: D 121 CYS cc_start: 0.7640 (t) cc_final: 0.7412 (t) REVERT: D 137 ARG cc_start: 0.7119 (tpp-160) cc_final: 0.6756 (tpp-160) REVERT: D 143 THR cc_start: 0.8066 (p) cc_final: 0.7564 (t) REVERT: D 148 CYS cc_start: 0.7889 (t) cc_final: 0.7513 (t) REVERT: D 188 MET cc_start: 0.7250 (mmm) cc_final: 0.6648 (mmm) REVERT: D 198 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7589 (mt) REVERT: D 204 CYS cc_start: 0.7637 (m) cc_final: 0.7216 (m) REVERT: D 234 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7262 (t80) REVERT: D 277 SER cc_start: 0.7725 (t) cc_final: 0.7462 (t) REVERT: D 284 LEU cc_start: 0.7976 (tp) cc_final: 0.7538 (tp) REVERT: E 45 MET cc_start: 0.4930 (tmm) cc_final: 0.4650 (mmm) outliers start: 25 outliers final: 19 residues processed: 242 average time/residue: 0.0920 time to fit residues: 28.9723 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 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 85 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.142124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120285 restraints weight = 13248.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124425 restraints weight = 6550.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127199 restraints weight = 3988.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129045 restraints weight = 2774.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130258 restraints weight = 2118.558| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 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 = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8681 Z= 0.241 Angle : 0.697 20.282 11807 Z= 0.358 Chirality : 0.046 0.169 1330 Planarity : 0.005 0.056 1509 Dihedral : 4.669 19.584 1201 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.10 % Allowed : 16.63 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.26), residues: 1096 helix: 1.21 (0.28), residues: 384 sheet: -0.67 (0.39), residues: 207 loop : -1.98 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.028 0.002 TYR D 59 PHE 0.023 0.002 PHE B 540 TRP 0.020 0.002 TRP B 427 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 8676) covalent geometry : angle 0.69699 (11797) SS BOND : bond 0.00514 ( 5) SS BOND : angle 0.69586 ( 10) hydrogen bonds : bond 0.04316 ( 357) hydrogen bonds : angle 4.41247 ( 1030) *********************** 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 261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.6583 (mmt) cc_final: 0.6094 (mmt) REVERT: B 496 PHE cc_start: 0.7542 (t80) cc_final: 0.7262 (t80) REVERT: B 500 PHE cc_start: 0.7155 (t80) cc_final: 0.6909 (t80) REVERT: B 558 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6155 (mm-30) REVERT: C 29 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7338 (tt) REVERT: C 30 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7266 (tpp80) REVERT: C 45 LEU cc_start: 0.7887 (tp) cc_final: 0.7647 (tt) REVERT: C 221 MET cc_start: 0.7428 (ttm) cc_final: 0.7103 (ttp) REVERT: C 274 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7601 (ttpt) REVERT: C 295 ASP cc_start: 0.7740 (m-30) cc_final: 0.6955 (m-30) REVERT: C 338 LYS cc_start: 0.8342 (tttm) cc_final: 0.8063 (tttm) REVERT: C 382 THR cc_start: 0.8111 (m) cc_final: 0.7885 (m) REVERT: D 61 MET cc_start: 0.7621 (ppp) cc_final: 0.6935 (ppp) REVERT: D 65 THR cc_start: 0.8558 (p) cc_final: 0.8309 (p) REVERT: D 118 ASP cc_start: 0.7159 (p0) cc_final: 0.6925 (p0) REVERT: D 121 CYS cc_start: 0.7657 (t) cc_final: 0.7439 (t) REVERT: D 137 ARG cc_start: 0.7174 (tpp-160) cc_final: 0.6867 (tpp-160) REVERT: D 143 THR cc_start: 0.8056 (p) cc_final: 0.7801 (t) REVERT: D 148 CYS cc_start: 0.7892 (t) cc_final: 0.7577 (t) REVERT: D 163 ASP cc_start: 0.7357 (p0) cc_final: 0.6947 (p0) REVERT: D 188 MET cc_start: 0.7301 (mmm) cc_final: 0.6927 (mmm) REVERT: D 198 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7660 (mt) REVERT: D 204 CYS cc_start: 0.7751 (m) cc_final: 0.7296 (m) REVERT: D 234 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6985 (t80) REVERT: D 277 SER cc_start: 0.7698 (t) cc_final: 0.7414 (t) REVERT: D 284 LEU cc_start: 0.8043 (tp) cc_final: 0.7803 (tp) REVERT: E 45 MET cc_start: 0.4950 (tmm) cc_final: 0.4664 (mmm) outliers start: 27 outliers final: 20 residues processed: 246 average time/residue: 0.0842 time to fit residues: 27.2790 Evaluate side-chains 255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 420 TRP Chi-restraints excluded: chain B residue 433 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 218 ASN 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 D residue 198 LEU 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 53 SER 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 105 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.143917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122240 restraints weight = 13068.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126308 restraints weight = 6564.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129003 restraints weight = 4033.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130887 restraints weight = 2816.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132054 restraints weight = 2148.592| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 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 = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2155 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= 0.183 Angle : 0.677 20.160 11807 Z= 0.343 Chirality : 0.044 0.160 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.633 19.327 1201 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.87 % Allowed : 17.66 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.26), residues: 1096 helix: 1.21 (0.28), residues: 385 sheet: -0.78 (0.38), residues: 214 loop : -1.94 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 49 TYR 0.026 0.002 TYR B 498 PHE 0.029 0.002 PHE B 556 TRP 0.019 0.002 TRP B 427 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8676) covalent geometry : angle 0.67677 (11797) SS BOND : bond 0.00391 ( 5) SS BOND : angle 0.56138 ( 10) hydrogen bonds : bond 0.03966 ( 357) hydrogen bonds : angle 4.33400 ( 1030) *********************** 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 258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 407 MET cc_start: 0.6630 (mmt) cc_final: 0.6123 (mmt) REVERT: B 496 PHE cc_start: 0.7599 (t80) cc_final: 0.7360 (t80) REVERT: B 500 PHE cc_start: 0.7150 (t80) cc_final: 0.6901 (t80) REVERT: B 558 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6141 (mm-30) REVERT: C 29 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7327 (tt) REVERT: C 30 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7311 (tpp80) REVERT: C 221 MET cc_start: 0.7423 (ttm) cc_final: 0.7098 (ttp) REVERT: C 274 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7597 (ttpt) REVERT: C 295 ASP cc_start: 0.7588 (m-30) cc_final: 0.6857 (m-30) REVERT: C 338 LYS cc_start: 0.8311 (tttm) cc_final: 0.8053 (tttm) REVERT: C 382 THR cc_start: 0.8103 (m) cc_final: 0.7847 (m) REVERT: C 385 GLN cc_start: 0.8151 (tp40) cc_final: 0.7884 (mm-40) REVERT: D 17 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 61 MET cc_start: 0.7588 (ppp) cc_final: 0.7061 (ppp) REVERT: D 65 THR cc_start: 0.8577 (p) cc_final: 0.8309 (p) REVERT: D 118 ASP cc_start: 0.7095 (p0) cc_final: 0.6870 (p0) REVERT: D 121 CYS cc_start: 0.7578 (t) cc_final: 0.7372 (t) REVERT: D 137 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6846 (tpp-160) REVERT: D 143 THR cc_start: 0.8027 (p) cc_final: 0.7653 (t) REVERT: D 148 CYS cc_start: 0.7871 (t) cc_final: 0.7557 (t) REVERT: D 188 MET cc_start: 0.7217 (mmm) cc_final: 0.6881 (mmm) REVERT: D 198 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7617 (mt) REVERT: D 204 CYS cc_start: 0.7675 (m) cc_final: 0.7246 (m) REVERT: D 234 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6946 (t80) REVERT: D 277 SER cc_start: 0.7669 (t) cc_final: 0.7384 (t) REVERT: D 284 LEU cc_start: 0.8009 (tp) cc_final: 0.7763 (tp) outliers start: 25 outliers final: 20 residues processed: 241 average time/residue: 0.0852 time to fit residues: 27.1475 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 25 LYS 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 314 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 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 = 0.3844 r_free = 0.3844 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121521 restraints weight = 13092.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125527 restraints weight = 6584.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128276 restraints weight = 4056.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130125 restraints weight = 2834.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131356 restraints weight = 2162.649| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- 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: 0.7041 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8681 Z= 0.215 Angle : 0.704 20.566 11807 Z= 0.357 Chirality : 0.045 0.164 1330 Planarity : 0.005 0.056 1509 Dihedral : 4.739 20.366 1201 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.10 % Allowed : 17.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.26), residues: 1096 helix: 1.15 (0.28), residues: 385 sheet: -0.79 (0.38), residues: 214 loop : -1.98 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 49 TYR 0.024 0.002 TYR B 498 PHE 0.029 0.002 PHE B 556 TRP 0.021 0.002 TRP B 427 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8676) covalent geometry : angle 0.70449 (11797) SS BOND : bond 0.00455 ( 5) SS BOND : angle 0.65567 ( 10) hydrogen bonds : bond 0.04154 ( 357) hydrogen bonds : angle 4.39181 ( 1030) *********************** 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 259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 407 MET cc_start: 0.6634 (mmt) cc_final: 0.6128 (mmt) REVERT: B 500 PHE cc_start: 0.7157 (t80) cc_final: 0.6913 (t80) REVERT: B 558 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6176 (mm-30) REVERT: C 29 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7363 (tt) REVERT: C 30 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7300 (tpp80) REVERT: C 221 MET cc_start: 0.7427 (ttm) cc_final: 0.7118 (ttp) REVERT: C 274 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7595 (ttpt) REVERT: C 295 ASP cc_start: 0.7632 (m-30) cc_final: 0.6936 (m-30) REVERT: C 338 LYS cc_start: 0.8336 (tttm) cc_final: 0.8059 (tttm) REVERT: C 382 THR cc_start: 0.8103 (m) cc_final: 0.7850 (m) REVERT: C 385 GLN cc_start: 0.8151 (tp40) cc_final: 0.7898 (mm-40) REVERT: D 17 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8264 (tm-30) REVERT: D 61 MET cc_start: 0.7607 (ppp) cc_final: 0.7112 (ppp) REVERT: D 65 THR cc_start: 0.8593 (p) cc_final: 0.8329 (p) REVERT: D 118 ASP cc_start: 0.7123 (p0) cc_final: 0.6905 (p0) REVERT: D 121 CYS cc_start: 0.7585 (t) cc_final: 0.7383 (t) REVERT: D 143 THR cc_start: 0.7988 (p) cc_final: 0.7746 (t) REVERT: D 148 CYS cc_start: 0.7883 (t) cc_final: 0.7561 (t) REVERT: D 163 ASP cc_start: 0.7365 (p0) cc_final: 0.7037 (p0) REVERT: D 188 MET cc_start: 0.7248 (mmm) cc_final: 0.6916 (mmm) REVERT: D 198 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (mt) REVERT: D 204 CYS cc_start: 0.7721 (m) cc_final: 0.7265 (m) REVERT: D 234 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6856 (t80) REVERT: D 277 SER cc_start: 0.7733 (t) cc_final: 0.7457 (t) REVERT: D 284 LEU cc_start: 0.8032 (tp) cc_final: 0.7768 (tp) REVERT: N 133 VAL cc_start: 0.8105 (t) cc_final: 0.7828 (p) outliers start: 27 outliers final: 22 residues processed: 240 average time/residue: 0.0881 time to fit residues: 27.5569 Evaluate side-chains 255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 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 314 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 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 81 ILE 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 67 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 HIS D 110 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 = 0.3870 r_free = 0.3870 target = 0.145157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123597 restraints weight = 13016.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127695 restraints weight = 6543.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130407 restraints weight = 4012.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132216 restraints weight = 2804.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133491 restraints weight = 2151.054| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2278 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= 0.143 Angle : 0.680 20.601 11807 Z= 0.338 Chirality : 0.043 0.155 1330 Planarity : 0.005 0.057 1509 Dihedral : 4.607 22.195 1201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.87 % Allowed : 18.58 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.26), residues: 1096 helix: 1.28 (0.28), residues: 383 sheet: -0.75 (0.37), residues: 220 loop : -1.85 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.025 0.002 TYR B 498 PHE 0.029 0.002 PHE B 556 TRP 0.018 0.002 TRP B 420 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8676) covalent geometry : angle 0.68040 (11797) SS BOND : bond 0.00281 ( 5) SS BOND : angle 0.55515 ( 10) hydrogen bonds : bond 0.03709 ( 357) hydrogen bonds : angle 4.25090 ( 1030) ********************** 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 261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 406 PHE cc_start: 0.8227 (t80) cc_final: 0.7901 (t80) REVERT: B 407 MET cc_start: 0.6605 (mmt) cc_final: 0.6108 (mmt) REVERT: B 435 TRP cc_start: 0.6543 (t60) cc_final: 0.6194 (t60) REVERT: B 500 PHE cc_start: 0.7107 (t80) cc_final: 0.6860 (t80) REVERT: B 558 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6084 (mm-30) REVERT: C 29 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7296 (tt) REVERT: C 221 MET cc_start: 0.7410 (ttm) cc_final: 0.7139 (ttm) REVERT: C 274 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7580 (ttpt) REVERT: C 295 ASP cc_start: 0.7623 (m-30) cc_final: 0.6918 (m-30) REVERT: C 300 LYS cc_start: 0.7842 (tttm) cc_final: 0.7483 (tttp) REVERT: C 338 LYS cc_start: 0.8286 (tttm) cc_final: 0.8025 (tttm) REVERT: C 382 THR cc_start: 0.8084 (m) cc_final: 0.7856 (m) REVERT: D 17 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 61 MET cc_start: 0.7606 (ppp) cc_final: 0.7321 (ppp) REVERT: D 65 THR cc_start: 0.8585 (p) cc_final: 0.8317 (p) REVERT: D 111 TYR cc_start: 0.8159 (m-80) cc_final: 0.7924 (m-80) REVERT: D 118 ASP cc_start: 0.7082 (p0) cc_final: 0.6857 (p0) REVERT: D 143 THR cc_start: 0.7953 (p) cc_final: 0.7724 (t) REVERT: D 148 CYS cc_start: 0.7868 (t) cc_final: 0.7541 (t) REVERT: D 163 ASP cc_start: 0.7227 (p0) cc_final: 0.6902 (p0) REVERT: D 188 MET cc_start: 0.7203 (mmm) cc_final: 0.6826 (mmm) REVERT: D 204 CYS cc_start: 0.7591 (m) cc_final: 0.7213 (m) REVERT: D 219 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7655 (tpp80) REVERT: D 234 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6903 (t80) REVERT: D 277 SER cc_start: 0.7730 (t) cc_final: 0.7437 (t) REVERT: D 284 LEU cc_start: 0.7985 (tp) cc_final: 0.7541 (tp) REVERT: D 304 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7791 (ptm160) REVERT: N 145 THR cc_start: 0.7661 (p) cc_final: 0.7451 (p) outliers start: 25 outliers final: 20 residues processed: 243 average time/residue: 0.0850 time to fit residues: 27.1468 Evaluate side-chains 251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 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 320 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain 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 80 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.143345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122257 restraints weight = 13060.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126170 restraints weight = 6717.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128816 restraints weight = 4170.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130568 restraints weight = 2932.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131669 restraints weight = 2264.566| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2319 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= 0.182 Angle : 0.697 20.390 11807 Z= 0.350 Chirality : 0.044 0.154 1330 Planarity : 0.005 0.056 1509 Dihedral : 4.649 21.651 1201 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.64 % Allowed : 19.15 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.26), residues: 1096 helix: 1.27 (0.28), residues: 383 sheet: -0.70 (0.38), residues: 220 loop : -1.87 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 49 TYR 0.026 0.002 TYR B 498 PHE 0.029 0.002 PHE B 556 TRP 0.026 0.002 TRP B 620 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8676) covalent geometry : angle 0.69716 (11797) SS BOND : bond 0.00373 ( 5) SS BOND : angle 0.59553 ( 10) hydrogen bonds : bond 0.03943 ( 357) hydrogen bonds : angle 4.29516 ( 1030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.24 seconds wall clock time: 24 minutes 53.98 seconds (1493.98 seconds total)