Starting phenix.real_space_refine on Wed Feb 4 01:57:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.map" model { file = "/net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opz_70731/02_2026/9opz_70731.cif" } resolution = 3.16 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= -0.003 sd= 0.101 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: 5 Type Number sf(0) Gaussians S 59 5.16 5 Cl 3 4.86 5 C 5180 2.51 5 N 1386 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8147 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4037 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 22, 'TRANS': 478} Chain breaks: 2 Chain: "B" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4087 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 26, 'TRANS': 496} Chain breaks: 2 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'RRJ': 1, 'RRY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.24 Number of scatterers: 8147 At special positions: 0 Unit cell: (94.754, 84.37, 125.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 59 16.00 O 1519 8.00 N 1386 7.00 C 5180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 559 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ?1-2 " RRY C 1 " - " RRJ C 2 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 309.2 milliseconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 39.9% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.681A pdb=" N TYR A 62 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.760A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.007A pdb=" N PHE A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.644A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.909A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.602A pdb=" N LYS A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 4.120A pdb=" N LEU A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.752A pdb=" N PHE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 380 removed outlier: 3.690A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.629A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.897A pdb=" N ASN B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.880A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.774A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.786A pdb=" N PHE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.650A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 176 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.658A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.949A pdb=" N ASN B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.348A pdb=" N VAL B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 311 removed outlier: 4.034A pdb=" N MET B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.738A pdb=" N ASP B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 375 " --> pdb=" O CYS B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.963A pdb=" N GLN B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 415 removed outlier: 3.770A pdb=" N ILE B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 398 " --> pdb=" O HIS B 394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.837A pdb=" N LEU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.536A pdb=" N MET B 492 " --> pdb=" O GLN B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.240A pdb=" N TYR A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU A 97 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ILE A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.540A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 271 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 466 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN A 452 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER A 464 " --> pdb=" O GLN A 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 431 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.383A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE B 100 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY B 39 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 140 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 237 removed outlier: 7.670A pdb=" N VAL B 243 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY B 213 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 237 removed outlier: 7.104A pdb=" N TRP B 208 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 272 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 210 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 274 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 212 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL B 321 " --> pdb=" O TRP B 466 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR B 461 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 480 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 463 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AB4, first strand: chain 'B' and resid 512 through 513 Processing sheet with id=AB5, first strand: chain 'B' and resid 516 through 517 Processing sheet with id=AB6, first strand: chain 'B' and resid 533 through 535 304 hydrogen bonds defined for protein. 834 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: 1.43 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2440 1.34 - 1.46: 1683 1.46 - 1.58: 4138 1.58 - 1.70: 0 1.70 - 1.83: 85 Bond restraints: 8346 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.235 1.223 0.012 4.70e-03 4.53e+04 6.06e+00 bond pdb=" C2 RRY C 1 " pdb=" O2 RRY C 1 " ideal model delta sigma weight residual 1.383 1.427 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C LEU B 283 " pdb=" O LEU B 283 " ideal model delta sigma weight residual 1.237 1.212 0.024 1.17e-02 7.31e+03 4.29e+00 bond pdb=" C ALA B 277 " pdb=" O ALA B 277 " ideal model delta sigma weight residual 1.237 1.214 0.022 1.17e-02 7.31e+03 3.63e+00 bond pdb=" N LEU B 23 " pdb=" CA LEU B 23 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 ... (remaining 8341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 10413 1.05 - 2.10: 766 2.10 - 3.15: 121 3.15 - 4.21: 46 4.21 - 5.26: 11 Bond angle restraints: 11357 Sorted by residual: angle pdb=" N ALA B 277 " pdb=" CA ALA B 277 " pdb=" C ALA B 277 " ideal model delta sigma weight residual 111.28 116.00 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ALA A 43 " pdb=" CA ALA A 43 " pdb=" C ALA A 43 " ideal model delta sigma weight residual 111.24 115.40 -4.16 1.29e+00 6.01e-01 1.04e+01 angle pdb=" N SER A 165 " pdb=" CA SER A 165 " pdb=" CB SER A 165 " ideal model delta sigma weight residual 113.65 109.28 4.37 1.47e+00 4.63e-01 8.82e+00 angle pdb=" N THR B 132 " pdb=" CA THR B 132 " pdb=" C THR B 132 " ideal model delta sigma weight residual 112.72 108.81 3.91 1.36e+00 5.41e-01 8.26e+00 angle pdb=" N VAL B 424 " pdb=" CA VAL B 424 " pdb=" C VAL B 424 " ideal model delta sigma weight residual 111.91 109.36 2.55 8.90e-01 1.26e+00 8.20e+00 ... (remaining 11352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4636 17.28 - 34.56: 318 34.56 - 51.84: 55 51.84 - 69.11: 15 69.11 - 86.39: 7 Dihedral angle restraints: 5031 sinusoidal: 2030 harmonic: 3001 Sorted by residual: dihedral pdb=" CB CYS B 529 " pdb=" SG CYS B 529 " pdb=" SG CYS B 543 " pdb=" CB CYS B 543 " ideal model delta sinusoidal sigma weight residual 93.00 155.61 -62.61 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ALA A 43 " pdb=" C ALA A 43 " pdb=" N ASN A 44 " pdb=" CA ASN A 44 " ideal model delta harmonic sigma weight residual 180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN B 133 " pdb=" C GLN B 133 " pdb=" N TYR B 134 " pdb=" CA TYR B 134 " ideal model delta harmonic sigma weight residual -180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 5028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 763 0.031 - 0.061: 343 0.061 - 0.092: 97 0.092 - 0.123: 60 0.123 - 0.153: 9 Chirality restraints: 1272 Sorted by residual: chirality pdb=" C2 RRY C 1 " pdb=" C1 RRY C 1 " pdb=" C3 RRY C 1 " pdb=" O5 RRY C 1 " both_signs ideal model delta sigma weight residual False 2.66 2.51 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA VAL B 467 " pdb=" N VAL B 467 " pdb=" C VAL B 467 " pdb=" CB VAL B 467 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA PRO A 417 " pdb=" N PRO A 417 " pdb=" C PRO A 417 " pdb=" CB PRO A 417 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1269 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 401 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C TYR B 401 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR B 401 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 402 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 544 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 545 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 105 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 106 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " 0.022 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1944 2.79 - 3.32: 7895 3.32 - 3.84: 12871 3.84 - 4.37: 16104 4.37 - 4.90: 26986 Nonbonded interactions: 65800 Sorted by model distance: nonbonded pdb=" CB ALA B 316 " pdb=" CH2 TRP B 468 " model vdw 2.262 3.760 nonbonded pdb=" NH1 ARG B 327 " pdb=" OD1 ASP B 462 " model vdw 2.310 3.120 nonbonded pdb=" O LEU B 331 " pdb=" CD1 LEU B 331 " model vdw 2.332 3.460 nonbonded pdb=" O TYR A 164 " pdb=" OG SER A 165 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASP B 540 " pdb=" N PHE B 541 " model vdw 2.347 3.120 ... (remaining 65795 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.960 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.003 0.044 8363 Z= 0.171 Angle : 0.648 8.527 11392 Z= 0.367 Chirality : 0.042 0.153 1272 Planarity : 0.005 0.040 1463 Dihedral : 12.723 86.393 3037 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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 are not related in a simple way. whole: -0.68 (0.25), residues: 1012 helix: 0.03 (0.27), residues: 314 sheet: -0.58 (0.39), residues: 168 loop : -0.61 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 378 TYR 0.019 0.002 TYR A 389 PHE 0.011 0.001 PHE B 157 TRP 0.012 0.001 TRP B 303 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8346) covalent geometry : angle 0.64070 (11357) SS BOND : bond 0.00195 ( 16) SS BOND : angle 1.03767 ( 32) hydrogen bonds : bond 0.15465 ( 303) hydrogen bonds : angle 6.59440 ( 834) glycosidic custom : bond 0.02993 ( 1) glycosidic custom : angle 5.28250 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8764 (mm) cc_final: 0.8387 (mt) REVERT: A 157 PHE cc_start: 0.8937 (m-80) cc_final: 0.8644 (m-80) REVERT: A 173 ASP cc_start: 0.8037 (t0) cc_final: 0.7807 (t0) REVERT: A 516 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8024 (mm-30) REVERT: B 155 LYS cc_start: 0.8274 (tptp) cc_final: 0.7792 (mtmt) REVERT: B 465 MET cc_start: 0.7740 (ttt) cc_final: 0.7442 (ttt) REVERT: B 488 GLN cc_start: 0.7759 (mt0) cc_final: 0.7537 (mm-40) REVERT: B 536 LYS cc_start: 0.7384 (ttmt) cc_final: 0.6829 (tptt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1077 time to fit residues: 23.7355 Evaluate side-chains 106 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.194214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153981 restraints weight = 10541.949| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.94 r_work: 0.3662 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8363 Z= 0.168 Angle : 0.626 7.778 11392 Z= 0.335 Chirality : 0.045 0.166 1272 Planarity : 0.004 0.039 1463 Dihedral : 5.872 58.979 1142 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.87 % Allowed : 8.56 % Favored : 89.57 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1012 helix: 0.55 (0.27), residues: 330 sheet: -0.66 (0.39), residues: 173 loop : -0.50 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 327 TYR 0.016 0.002 TYR A 389 PHE 0.010 0.002 PHE A 236 TRP 0.023 0.002 TRP B 468 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8346) covalent geometry : angle 0.62107 (11357) SS BOND : bond 0.00274 ( 16) SS BOND : angle 1.66274 ( 32) hydrogen bonds : bond 0.05029 ( 303) hydrogen bonds : angle 4.66008 ( 834) glycosidic custom : bond 0.00090 ( 1) glycosidic custom : angle 0.70041 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.5458 (tpp) cc_final: 0.4743 (tpt) REVERT: A 115 LEU cc_start: 0.8727 (mm) cc_final: 0.8347 (mt) REVERT: A 173 ASP cc_start: 0.7986 (t0) cc_final: 0.7741 (t0) REVERT: A 504 LYS cc_start: 0.8471 (pttt) cc_final: 0.8092 (pttp) REVERT: A 516 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8053 (mm-30) REVERT: B 134 TYR cc_start: 0.5948 (t80) cc_final: 0.5406 (t80) REVERT: B 155 LYS cc_start: 0.7946 (tptp) cc_final: 0.7466 (mtmt) REVERT: B 233 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7615 (mtp85) REVERT: B 240 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: B 310 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6169 (ptp) REVERT: B 465 MET cc_start: 0.7906 (ttt) cc_final: 0.7619 (ttt) REVERT: B 488 GLN cc_start: 0.7632 (mt0) cc_final: 0.7234 (mm-40) REVERT: B 498 GLN cc_start: 0.7717 (pp30) cc_final: 0.7292 (pp30) REVERT: B 536 LYS cc_start: 0.7341 (ttmt) cc_final: 0.6885 (tptt) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 0.1011 time to fit residues: 17.7541 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 HIS B 436 ASN B 520 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143989 restraints weight = 10203.627| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.71 r_work: 0.3434 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8363 Z= 0.121 Angle : 0.545 8.195 11392 Z= 0.288 Chirality : 0.043 0.214 1272 Planarity : 0.004 0.039 1463 Dihedral : 5.255 55.176 1142 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.52 % Allowed : 9.77 % Favored : 87.71 % 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 are not related in a simple way. whole: -0.02 (0.26), residues: 1012 helix: 1.16 (0.28), residues: 318 sheet: -0.82 (0.39), residues: 182 loop : -0.37 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 327 TYR 0.014 0.002 TYR B 281 PHE 0.010 0.001 PHE A 335 TRP 0.019 0.002 TRP B 303 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8346) covalent geometry : angle 0.54210 (11357) SS BOND : bond 0.00220 ( 16) SS BOND : angle 1.16826 ( 32) hydrogen bonds : bond 0.04138 ( 303) hydrogen bonds : angle 4.31923 ( 834) glycosidic custom : bond 0.00023 ( 1) glycosidic custom : angle 0.82612 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.325 Fit side-chains REVERT: A 58 MET cc_start: 0.5563 (tpp) cc_final: 0.4753 (tpt) REVERT: A 494 MET cc_start: 0.8839 (mtt) cc_final: 0.8607 (mtt) REVERT: A 504 LYS cc_start: 0.8388 (pttt) cc_final: 0.8070 (pttp) REVERT: A 516 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7743 (mm-30) REVERT: B 134 TYR cc_start: 0.5865 (t80) cc_final: 0.5518 (t80) REVERT: B 155 LYS cc_start: 0.8006 (tptp) cc_final: 0.7421 (mtmt) REVERT: B 240 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: B 465 MET cc_start: 0.7888 (ttt) cc_final: 0.7556 (ttt) REVERT: B 488 GLN cc_start: 0.7475 (mt0) cc_final: 0.7099 (mm-40) REVERT: B 498 GLN cc_start: 0.7635 (pp30) cc_final: 0.7217 (pp30) REVERT: B 530 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8408 (mmmt) REVERT: B 536 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6654 (tptt) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.0980 time to fit residues: 16.4842 Evaluate side-chains 104 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143631 restraints weight = 10442.480| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.80 r_work: 0.3425 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8363 Z= 0.127 Angle : 0.556 10.179 11392 Z= 0.288 Chirality : 0.042 0.141 1272 Planarity : 0.004 0.036 1463 Dihedral : 5.066 50.840 1142 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.63 % Allowed : 11.09 % Favored : 86.28 % 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 are not related in a simple way. whole: 0.21 (0.27), residues: 1012 helix: 1.57 (0.29), residues: 312 sheet: -0.84 (0.39), residues: 180 loop : -0.30 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 535 TYR 0.014 0.001 TYR B 281 PHE 0.009 0.001 PHE B 65 TRP 0.019 0.002 TRP B 303 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8346) covalent geometry : angle 0.55090 (11357) SS BOND : bond 0.00320 ( 16) SS BOND : angle 1.51222 ( 32) hydrogen bonds : bond 0.04017 ( 303) hydrogen bonds : angle 4.15877 ( 834) glycosidic custom : bond 0.00064 ( 1) glycosidic custom : angle 0.57155 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.297 Fit side-chains REVERT: A 58 MET cc_start: 0.5531 (tpp) cc_final: 0.4838 (tpt) REVERT: A 147 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8412 (t) REVERT: A 494 MET cc_start: 0.8822 (mtt) cc_final: 0.8588 (mtt) REVERT: A 504 LYS cc_start: 0.8437 (pttt) cc_final: 0.8095 (pttp) REVERT: B 155 LYS cc_start: 0.8066 (tptp) cc_final: 0.7516 (mtmt) REVERT: B 240 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: B 310 MET cc_start: 0.6853 (pmm) cc_final: 0.6182 (pmm) REVERT: B 465 MET cc_start: 0.7908 (ttt) cc_final: 0.7610 (ttt) REVERT: B 488 GLN cc_start: 0.7556 (mt0) cc_final: 0.7066 (mm-40) REVERT: B 498 GLN cc_start: 0.7582 (pp30) cc_final: 0.7178 (pp30) REVERT: B 515 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7397 (ttp-170) REVERT: B 530 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8386 (mmmt) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.0944 time to fit residues: 15.4749 Evaluate side-chains 111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 533 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143585 restraints weight = 10353.819| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.72 r_work: 0.3420 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8363 Z= 0.130 Angle : 0.534 10.168 11392 Z= 0.277 Chirality : 0.042 0.140 1272 Planarity : 0.004 0.038 1463 Dihedral : 4.910 47.523 1142 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.85 % Allowed : 11.42 % Favored : 85.73 % 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 are not related in a simple way. whole: 0.25 (0.27), residues: 1012 helix: 1.64 (0.29), residues: 314 sheet: -0.94 (0.38), residues: 180 loop : -0.26 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 535 TYR 0.014 0.001 TYR B 401 PHE 0.009 0.001 PHE B 65 TRP 0.019 0.002 TRP B 303 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8346) covalent geometry : angle 0.52989 (11357) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.33998 ( 32) hydrogen bonds : bond 0.03924 ( 303) hydrogen bonds : angle 4.09096 ( 834) glycosidic custom : bond 0.00060 ( 1) glycosidic custom : angle 0.59420 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.324 Fit side-chains REVERT: A 58 MET cc_start: 0.5651 (tpp) cc_final: 0.5023 (tpt) REVERT: A 457 ARG cc_start: 0.8021 (mpt180) cc_final: 0.7740 (mpt180) REVERT: A 494 MET cc_start: 0.8807 (mtt) cc_final: 0.8587 (mtt) REVERT: A 504 LYS cc_start: 0.8476 (pttt) cc_final: 0.8137 (pttp) REVERT: B 25 LEU cc_start: 0.7451 (tp) cc_final: 0.7223 (tt) REVERT: B 155 LYS cc_start: 0.7978 (tptp) cc_final: 0.7568 (mtmt) REVERT: B 240 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 465 MET cc_start: 0.7937 (ttt) cc_final: 0.7626 (ttt) REVERT: B 488 GLN cc_start: 0.7726 (mt0) cc_final: 0.7203 (mm-40) REVERT: B 498 GLN cc_start: 0.7489 (pp30) cc_final: 0.7045 (pp30) REVERT: B 515 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7457 (ttp-170) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.0933 time to fit residues: 15.3848 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 83 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142193 restraints weight = 10280.989| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.72 r_work: 0.3433 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8363 Z= 0.144 Angle : 0.547 10.734 11392 Z= 0.282 Chirality : 0.042 0.140 1272 Planarity : 0.004 0.036 1463 Dihedral : 4.862 45.686 1142 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.18 % Allowed : 11.31 % Favored : 85.51 % 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 are not related in a simple way. whole: 0.18 (0.27), residues: 1012 helix: 1.62 (0.29), residues: 314 sheet: -1.01 (0.38), residues: 180 loop : -0.32 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 535 TYR 0.015 0.001 TYR B 401 PHE 0.009 0.001 PHE A 236 TRP 0.020 0.002 TRP B 303 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8346) covalent geometry : angle 0.54431 (11357) SS BOND : bond 0.00264 ( 16) SS BOND : angle 1.14424 ( 32) hydrogen bonds : bond 0.04013 ( 303) hydrogen bonds : angle 4.07031 ( 834) glycosidic custom : bond 0.00042 ( 1) glycosidic custom : angle 0.57979 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.332 Fit side-chains REVERT: A 58 MET cc_start: 0.5688 (tpp) cc_final: 0.5001 (tpt) REVERT: B 155 LYS cc_start: 0.7984 (tptp) cc_final: 0.7492 (mtmt) REVERT: B 240 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 310 MET cc_start: 0.6804 (pmm) cc_final: 0.6513 (pmm) REVERT: B 465 MET cc_start: 0.7946 (ttt) cc_final: 0.7569 (ttt) REVERT: B 488 GLN cc_start: 0.7763 (mt0) cc_final: 0.7167 (mm-40) REVERT: B 498 GLN cc_start: 0.7358 (pp30) cc_final: 0.6919 (pp30) REVERT: B 515 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7516 (ttp-170) outliers start: 29 outliers final: 24 residues processed: 118 average time/residue: 0.0918 time to fit residues: 15.2551 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143839 restraints weight = 10406.039| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.67 r_work: 0.3440 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8363 Z= 0.108 Angle : 0.519 10.001 11392 Z= 0.267 Chirality : 0.041 0.138 1272 Planarity : 0.003 0.036 1463 Dihedral : 4.753 45.574 1142 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.96 % Allowed : 12.07 % Favored : 84.96 % 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 are not related in a simple way. whole: 0.28 (0.27), residues: 1012 helix: 1.76 (0.29), residues: 316 sheet: -0.94 (0.39), residues: 178 loop : -0.32 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 535 TYR 0.014 0.001 TYR B 401 PHE 0.009 0.001 PHE B 65 TRP 0.017 0.002 TRP B 208 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8346) covalent geometry : angle 0.51473 (11357) SS BOND : bond 0.00181 ( 16) SS BOND : angle 1.28295 ( 32) hydrogen bonds : bond 0.03634 ( 303) hydrogen bonds : angle 3.92381 ( 834) glycosidic custom : bond 0.00081 ( 1) glycosidic custom : angle 0.65231 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.325 Fit side-chains REVERT: A 58 MET cc_start: 0.5611 (tpp) cc_final: 0.4955 (tpt) REVERT: A 494 MET cc_start: 0.8775 (mtt) cc_final: 0.8573 (mtt) REVERT: B 155 LYS cc_start: 0.7932 (tptp) cc_final: 0.7486 (mtmt) REVERT: B 240 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: B 465 MET cc_start: 0.7881 (ttt) cc_final: 0.7518 (ttt) REVERT: B 488 GLN cc_start: 0.7720 (mt0) cc_final: 0.7071 (mm-40) REVERT: B 498 GLN cc_start: 0.7294 (pp30) cc_final: 0.6779 (pp30) REVERT: B 515 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7403 (ttp-170) outliers start: 27 outliers final: 24 residues processed: 117 average time/residue: 0.0921 time to fit residues: 15.2591 Evaluate side-chains 116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141989 restraints weight = 10359.720| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.80 r_work: 0.3414 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8363 Z= 0.139 Angle : 0.541 9.385 11392 Z= 0.280 Chirality : 0.042 0.144 1272 Planarity : 0.004 0.035 1463 Dihedral : 4.782 43.547 1142 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.29 % Allowed : 12.40 % Favored : 84.30 % 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 are not related in a simple way. whole: 0.11 (0.27), residues: 1012 helix: 1.61 (0.29), residues: 316 sheet: -1.05 (0.39), residues: 180 loop : -0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.014 0.001 TYR B 401 PHE 0.014 0.001 PHE B 65 TRP 0.025 0.002 TRP B 303 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8346) covalent geometry : angle 0.53811 (11357) SS BOND : bond 0.00239 ( 16) SS BOND : angle 1.25228 ( 32) hydrogen bonds : bond 0.03947 ( 303) hydrogen bonds : angle 4.02988 ( 834) glycosidic custom : bond 0.00057 ( 1) glycosidic custom : angle 0.59603 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.322 Fit side-chains REVERT: A 58 MET cc_start: 0.5596 (tpp) cc_final: 0.5024 (tpt) REVERT: B 155 LYS cc_start: 0.7961 (tptp) cc_final: 0.7447 (mtmt) REVERT: B 240 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: B 465 MET cc_start: 0.7958 (ttt) cc_final: 0.7569 (ttt) REVERT: B 488 GLN cc_start: 0.7862 (mt0) cc_final: 0.7145 (mm-40) REVERT: B 498 GLN cc_start: 0.7276 (pp30) cc_final: 0.6763 (pp30) REVERT: B 515 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7478 (ttp-170) outliers start: 30 outliers final: 24 residues processed: 114 average time/residue: 0.0852 time to fit residues: 13.8274 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144405 restraints weight = 10255.727| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.52 r_work: 0.3470 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8363 Z= 0.123 Angle : 0.526 9.205 11392 Z= 0.271 Chirality : 0.041 0.140 1272 Planarity : 0.003 0.035 1463 Dihedral : 4.690 43.641 1142 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 12.62 % Favored : 84.41 % 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 are not related in a simple way. whole: 0.09 (0.27), residues: 1012 helix: 1.63 (0.29), residues: 316 sheet: -1.04 (0.39), residues: 180 loop : -0.46 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.015 0.001 TYR B 401 PHE 0.015 0.001 PHE B 65 TRP 0.023 0.002 TRP B 303 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8346) covalent geometry : angle 0.52333 (11357) SS BOND : bond 0.00207 ( 16) SS BOND : angle 1.13427 ( 32) hydrogen bonds : bond 0.03744 ( 303) hydrogen bonds : angle 3.96897 ( 834) glycosidic custom : bond 0.00071 ( 1) glycosidic custom : angle 0.59349 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.315 Fit side-chains REVERT: A 58 MET cc_start: 0.5701 (tpp) cc_final: 0.5125 (tpt) REVERT: B 155 LYS cc_start: 0.7933 (tptp) cc_final: 0.7522 (mtmt) REVERT: B 240 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: B 465 MET cc_start: 0.7902 (ttt) cc_final: 0.7547 (ttt) REVERT: B 488 GLN cc_start: 0.7833 (mt0) cc_final: 0.7123 (mm-40) REVERT: B 498 GLN cc_start: 0.7245 (pp30) cc_final: 0.6751 (pp30) outliers start: 27 outliers final: 23 residues processed: 114 average time/residue: 0.0929 time to fit residues: 14.7897 Evaluate side-chains 112 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 0.0170 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 HIS ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145083 restraints weight = 10260.679| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.54 r_work: 0.3472 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8363 Z= 0.113 Angle : 0.543 9.964 11392 Z= 0.280 Chirality : 0.042 0.190 1272 Planarity : 0.003 0.034 1463 Dihedral : 4.626 43.962 1142 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.85 % Allowed : 12.84 % Favored : 84.30 % 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 are not related in a simple way. whole: 0.09 (0.27), residues: 1012 helix: 1.64 (0.29), residues: 316 sheet: -1.07 (0.39), residues: 181 loop : -0.46 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 535 TYR 0.018 0.001 TYR B 401 PHE 0.016 0.001 PHE B 65 TRP 0.025 0.002 TRP B 303 HIS 0.010 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8346) covalent geometry : angle 0.54077 (11357) SS BOND : bond 0.00174 ( 16) SS BOND : angle 1.08963 ( 32) hydrogen bonds : bond 0.03710 ( 303) hydrogen bonds : angle 3.93946 ( 834) glycosidic custom : bond 0.00087 ( 1) glycosidic custom : angle 0.64273 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.321 Fit side-chains REVERT: A 58 MET cc_start: 0.5710 (tpp) cc_final: 0.5139 (tpt) REVERT: B 155 LYS cc_start: 0.7853 (tptp) cc_final: 0.7505 (mtmt) REVERT: B 240 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: B 405 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: B 465 MET cc_start: 0.7880 (ttt) cc_final: 0.7516 (ttt) REVERT: B 488 GLN cc_start: 0.7822 (mt0) cc_final: 0.7146 (mm-40) REVERT: B 498 GLN cc_start: 0.7235 (pp30) cc_final: 0.6753 (pp30) REVERT: B 537 HIS cc_start: 0.5973 (p90) cc_final: 0.5740 (p-80) outliers start: 26 outliers final: 20 residues processed: 112 average time/residue: 0.0831 time to fit residues: 13.2261 Evaluate side-chains 110 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** B 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.184565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147257 restraints weight = 10432.144| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.70 r_work: 0.3481 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8363 Z= 0.102 Angle : 0.546 9.880 11392 Z= 0.275 Chirality : 0.041 0.165 1272 Planarity : 0.003 0.035 1463 Dihedral : 4.538 44.100 1142 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.09 % Allowed : 13.61 % Favored : 84.30 % 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 are not related in a simple way. whole: 0.17 (0.27), residues: 1012 helix: 1.56 (0.29), residues: 323 sheet: -1.01 (0.40), residues: 179 loop : -0.34 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 535 TYR 0.019 0.001 TYR A 28 PHE 0.016 0.001 PHE B 65 TRP 0.021 0.002 TRP B 303 HIS 0.003 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8346) covalent geometry : angle 0.54366 (11357) SS BOND : bond 0.00159 ( 16) SS BOND : angle 1.01886 ( 32) hydrogen bonds : bond 0.03536 ( 303) hydrogen bonds : angle 3.89328 ( 834) glycosidic custom : bond 0.00096 ( 1) glycosidic custom : angle 0.66718 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.65 seconds wall clock time: 35 minutes 35.26 seconds (2135.26 seconds total)