Starting phenix.real_space_refine on Tue Apr 29 17:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.map" model { file = "/net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/04_2025/9c91_45359.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 Fe 5 7.16 5 P 4 5.49 5 S 31 5.16 5 C 5532 2.51 5 N 1545 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4119 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 518, 4093 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 496} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 518, 4093 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 496} Chain breaks: 1 bond proxies already assigned to first conformer: 4146 Chain: "B" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4504 Classifications: {'peptide': 570} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 542} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'FAD': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Unusual residues: {' K': 1, 'PO4': 1, 'SF4': 1, 'SRM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unsupported chir.volume_sign: {'cros': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7575 SG CYS B 434 31.093 38.242 41.422 1.00 35.39 S ATOM 7619 SG CYS B 440 30.295 43.097 45.770 1.00 39.39 S ATOM 7919 SG CYS B 479 25.725 42.645 42.397 1.00 45.34 S ATOM 7944 SG CYS B 483 31.365 44.001 39.596 1.00 61.15 S ATOM 7944 SG CYS B 483 31.365 44.001 39.596 1.00 61.15 S Time building chain proxies: 8.48, per 1000 atoms: 0.97 Number of scatterers: 8784 At special positions: 0 Unit cell: (77.265, 86.445, 139.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 K 1 19.00 S 31 16.00 P 4 15.00 O 1666 8.00 N 1545 7.00 C 5532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 603 " pdb="FE4 SF4 B 603 " - pdb=" SG CYS B 483 " pdb="FE2 SF4 B 603 " - pdb=" SG CYS B 440 " pdb="FE1 SF4 B 603 " - pdb=" SG CYS B 434 " pdb="FE3 SF4 B 603 " - pdb=" SG CYS B 479 " Number of angles added : 12 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 42.5% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.638A pdb=" N VAL A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 removed outlier: 5.357A pdb=" N ALA A 107 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.626A pdb=" N ALA A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 removed outlier: 4.358A pdb=" N GLY A 267 " --> pdb=" O GLY A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 267' Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.575A pdb=" N SER A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 463 removed outlier: 3.578A pdb=" N GLY A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.814A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.568A pdb=" N LYS A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 47 through 55 removed outlier: 4.854A pdb=" N ARG B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.807A pdb=" N HIS B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.517A pdb=" N ASN B 233 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.245A pdb=" N ALA B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.504A pdb=" N GLU B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 430' Processing helix chain 'B' and resid 450 through 465 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.690A pdb=" N ALA B 489 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.791A pdb=" N LYS B 540 " --> pdb=" O GLY B 536 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 542 " --> pdb=" O TRP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.649A pdb=" N LEU B 568 " --> pdb=" O PRO B 564 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 6.888A pdb=" N LEU A 112 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE A 151 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 114 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N VAL A 150 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP A 182 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N SER A 152 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 184 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279 removed outlier: 4.460A pdb=" N ARG A 436 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU A 241 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP A 262 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 255 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 518 removed outlier: 6.339A pdb=" N ASN A 483 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASP A 515 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 485 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA A 517 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 487 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 549 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 597 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 551 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR A 599 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 553 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.670A pdb=" N LEU B 82 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N HIS B 123 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.846A pdb=" N ASP B 389 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 402 " --> pdb=" O TRP B 356 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TRP B 356 " --> pdb=" O GLY B 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.335A pdb=" N LEU B 156 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 219 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA B 239 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 221 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA B 241 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU B 242 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 247 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE B 249 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR B 276 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 251 " --> pdb=" O PHE B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 431 through 433 removed outlier: 6.696A pdb=" N MET B 432 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR B 501 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 505 " --> pdb=" O MET B 517 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N MET B 517 " --> pdb=" O LEU B 505 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1006 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 3816 1.43 - 1.64: 5102 1.64 - 1.86: 46 1.86 - 2.07: 4 2.07 - 2.28: 12 Bond restraints: 8980 Sorted by residual: bond pdb=" C4 FMN A 601 " pdb=" C4A FMN A 601 " ideal model delta sigma weight residual 1.485 1.396 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3P FAD A 600 " pdb=" P FAD A 600 " ideal model delta sigma weight residual 1.660 1.578 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C4A FMN A 601 " pdb=" N5 FMN A 601 " ideal model delta sigma weight residual 1.300 1.379 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O5B FAD A 600 " pdb=" PA FAD A 600 " ideal model delta sigma weight residual 1.634 1.567 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O5' FAD A 600 " pdb=" P FAD A 600 " ideal model delta sigma weight residual 1.637 1.571 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 8975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11936 1.91 - 3.81: 197 3.81 - 5.72: 48 5.72 - 7.63: 19 7.63 - 9.53: 7 Bond angle restraints: 12207 Sorted by residual: angle pdb=" C SER B 436 " pdb=" CA SER B 436 " pdb=" CB SER B 436 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.83e+01 angle pdb=" C LYS A 90 " pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA SER B 436 " pdb=" C SER B 436 " pdb=" N PHE B 437 " ideal model delta sigma weight residual 119.52 116.86 2.66 7.90e-01 1.60e+00 1.13e+01 angle pdb=" CA GLU A 330 " pdb=" CB GLU A 330 " pdb=" CG GLU A 330 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 angle pdb=" C2B SRM B 604 " pdb=" C3B SRM B 604 " pdb=" C4B SRM B 604 " ideal model delta sigma weight residual 108.00 98.47 9.53 3.00e+00 1.11e-01 1.01e+01 ... (remaining 12202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 4997 28.18 - 56.36: 363 56.36 - 84.53: 35 84.53 - 112.71: 2 112.71 - 140.89: 1 Dihedral angle restraints: 5398 sinusoidal: 2253 harmonic: 3145 Sorted by residual: dihedral pdb=" C3B SRM B 604 " pdb=" C2B SRM B 604 " pdb=" CDB SRM B 604 " pdb=" CEB SRM B 604 " ideal model delta sinusoidal sigma weight residual -54.26 86.63 -140.89 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" CA ASN B 149 " pdb=" C ASN B 149 " pdb=" N ASP B 150 " pdb=" CA ASP B 150 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP B 202 " pdb=" CB ASP B 202 " pdb=" CG ASP B 202 " pdb=" OD1 ASP B 202 " ideal model delta sinusoidal sigma weight residual -30.00 -86.61 56.61 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 5395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 855 0.035 - 0.070: 325 0.070 - 0.105: 103 0.105 - 0.140: 38 0.140 - 0.175: 4 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CB ILE B 206 " pdb=" CA ILE B 206 " pdb=" CG1 ILE B 206 " pdb=" CG2 ILE B 206 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CB THR A 162 " pdb=" CA THR A 162 " pdb=" OG1 THR A 162 " pdb=" CG2 THR A 162 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" C2A SRM B 604 " pdb=" C1A SRM B 604 " pdb=" CDA SRM B 604 " pdb=" CMA SRM B 604 " both_signs ideal model delta sigma weight residual False 2.63 2.48 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 1322 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 335 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 336 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 336 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 336 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" NB SRM B 604 " -0.002 2.00e-02 2.50e+03 1.51e-02 2.84e+00 pdb=" C1B SRM B 604 " -0.011 2.00e-02 2.50e+03 pdb=" C2B SRM B 604 " 0.015 2.00e-02 2.50e+03 pdb=" C4A SRM B 604 " 0.019 2.00e-02 2.50e+03 pdb=" CHB SRM B 604 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 131 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO B 132 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.023 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 1956 2.78 - 3.37: 9633 3.37 - 3.96: 17728 3.96 - 4.55: 25236 4.55 - 5.14: 37320 Nonbonded interactions: 91873 Sorted by model distance: nonbonded pdb=" OH TYR A 270 " pdb=" O GLU A 400 " model vdw 2.194 3.040 nonbonded pdb=" O GLU B 287 " pdb=" OG1 THR B 291 " model vdw 2.217 3.040 nonbonded pdb=" O GLU A 109 " pdb=" OG1 THR A 146 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 252 " pdb=" OD1 ASP A 495 " model vdw 2.248 3.040 nonbonded pdb=" O GLY A 463 " pdb=" OG SER A 552 " model vdw 2.256 3.040 ... (remaining 91868 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=0.18 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0042 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 : 0.005 0.089 8987 Z= 0.210 Angle : 0.757 19.584 12219 Z= 0.321 Chirality : 0.043 0.175 1325 Planarity : 0.004 0.051 1590 Dihedral : 18.115 140.888 3376 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 27.80 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1086 helix: 1.40 (0.28), residues: 389 sheet: -0.34 (0.37), residues: 203 loop : -0.46 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 295 HIS 0.002 0.001 HIS B 55 PHE 0.016 0.002 PHE A 103 TYR 0.019 0.001 TYR A 332 ARG 0.005 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.16652 ( 355) hydrogen bonds : angle 6.99197 ( 1006) metal coordination : bond 0.01592 ( 4) metal coordination : angle 9.90915 ( 12) covalent geometry : bond 0.00456 ( 8980) covalent geometry : angle 0.69069 (12207) Misc. bond : bond 0.02842 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ILE cc_start: -0.0194 (mt) cc_final: -0.1597 (mm) REVERT: A 592 ARG cc_start: 0.0616 (mmm160) cc_final: -0.1205 (ttm170) REVERT: B 135 GLN cc_start: 0.0618 (mm110) cc_final: -0.0438 (pt0) REVERT: B 136 MET cc_start: 0.2872 (pp-130) cc_final: 0.1155 (mmm) REVERT: B 192 TRP cc_start: 0.0643 (m100) cc_final: 0.0288 (m100) REVERT: B 439 THR cc_start: -0.0495 (OUTLIER) cc_final: -0.0715 (p) outliers start: 24 outliers final: 5 residues processed: 86 average time/residue: 0.9272 time to fit residues: 87.7143 Evaluate side-chains 52 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 439 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 40.0000 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 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 = 0.5015 r_free = 0.5015 target = 0.294044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.212142 restraints weight = 20046.520| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 5.57 r_work: 0.4011 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0189 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8987 Z= 0.188 Angle : 0.870 18.599 12219 Z= 0.391 Chirality : 0.047 0.203 1325 Planarity : 0.006 0.053 1590 Dihedral : 7.612 139.200 1281 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 5.16 % Allowed : 25.16 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1086 helix: 1.17 (0.27), residues: 391 sheet: -0.36 (0.36), residues: 191 loop : -0.66 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 542 HIS 0.010 0.001 HIS B 55 PHE 0.023 0.003 PHE B 122 TYR 0.020 0.002 TYR A 527 ARG 0.009 0.001 ARG A 596 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 355) hydrogen bonds : angle 5.64872 ( 1006) metal coordination : bond 0.01758 ( 4) metal coordination : angle 11.39388 ( 12) covalent geometry : bond 0.00415 ( 8980) covalent geometry : angle 0.79380 (12207) Misc. bond : bond 0.01282 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 47 time to evaluate : 0.840 Fit side-chains REVERT: A 104 LYS cc_start: 0.0216 (OUTLIER) cc_final: -0.0270 (mtpt) REVERT: A 545 ASP cc_start: 0.1837 (m-30) cc_final: 0.1425 (t70) REVERT: A 582 ASP cc_start: 0.2254 (t0) cc_final: 0.1987 (t70) REVERT: A 591 GLU cc_start: -0.0621 (OUTLIER) cc_final: -0.1101 (tp30) REVERT: A 592 ARG cc_start: -0.0507 (mmm160) cc_final: -0.2291 (mtt90) REVERT: B 125 ILE cc_start: -0.4809 (OUTLIER) cc_final: -0.5588 (pp) REVERT: B 126 LEU cc_start: -0.0101 (OUTLIER) cc_final: -0.0396 (mm) REVERT: B 136 MET cc_start: 0.2895 (OUTLIER) cc_final: 0.0815 (mmm) REVERT: B 413 LYS cc_start: 0.2949 (OUTLIER) cc_final: 0.2386 (mmtt) REVERT: B 432 MET cc_start: 0.2878 (mtt) cc_final: 0.2666 (mmt) REVERT: B 533 GLU cc_start: 0.2593 (OUTLIER) cc_final: 0.2105 (tp30) outliers start: 47 outliers final: 14 residues processed: 89 average time/residue: 0.9356 time to fit residues: 90.9640 Evaluate side-chains 61 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.0270 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 129 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.294901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.241167 restraints weight = 23979.603| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 3.93 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4585 r_free = 0.4585 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0611 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8987 Z= 0.161 Angle : 0.814 24.496 12219 Z= 0.352 Chirality : 0.044 0.148 1325 Planarity : 0.006 0.053 1590 Dihedral : 7.432 137.221 1274 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 4.29 % Allowed : 25.16 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1086 helix: 1.11 (0.27), residues: 393 sheet: -0.32 (0.38), residues: 184 loop : -0.71 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.006 0.001 HIS B 134 PHE 0.044 0.002 PHE A 486 TYR 0.021 0.002 TYR B 370 ARG 0.007 0.001 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 355) hydrogen bonds : angle 5.37938 ( 1006) metal coordination : bond 0.00986 ( 4) metal coordination : angle 11.27733 ( 12) covalent geometry : bond 0.00362 ( 8980) covalent geometry : angle 0.73401 (12207) Misc. bond : bond 0.02191 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.0531 (mp) REVERT: A 582 ASP cc_start: 0.3276 (t0) cc_final: 0.2661 (t70) REVERT: B 136 MET cc_start: 0.3251 (OUTLIER) cc_final: 0.1186 (mmm) REVERT: B 203 GLU cc_start: 0.1872 (OUTLIER) cc_final: 0.0021 (pt0) REVERT: B 413 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2132 (mmtt) REVERT: B 487 MET cc_start: 0.3117 (mpp) cc_final: 0.2332 (mmm) REVERT: B 533 GLU cc_start: 0.2901 (OUTLIER) cc_final: 0.2376 (tp30) outliers start: 39 outliers final: 20 residues processed: 77 average time/residue: 0.9586 time to fit residues: 80.7555 Evaluate side-chains 66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 88 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.301294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.247332 restraints weight = 16780.081| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 2.78 r_work: 0.4293 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0285 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8987 Z= 0.127 Angle : 0.757 23.147 12219 Z= 0.316 Chirality : 0.044 0.350 1325 Planarity : 0.005 0.057 1590 Dihedral : 7.393 142.558 1274 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 4.29 % Allowed : 24.40 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1086 helix: 1.30 (0.27), residues: 392 sheet: -0.38 (0.38), residues: 184 loop : -0.66 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 540 HIS 0.006 0.001 HIS B 134 PHE 0.016 0.002 PHE A 584 TYR 0.015 0.001 TYR B 370 ARG 0.003 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 355) hydrogen bonds : angle 5.05628 ( 1006) metal coordination : bond 0.00716 ( 4) metal coordination : angle 11.46403 ( 12) covalent geometry : bond 0.00286 ( 8980) covalent geometry : angle 0.66656 (12207) Misc. bond : bond 0.01343 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: -0.0334 (OUTLIER) cc_final: -0.0690 (mm-30) REVERT: A 444 ASN cc_start: 0.0638 (OUTLIER) cc_final: -0.0349 (p0) REVERT: A 545 ASP cc_start: 0.2100 (m-30) cc_final: 0.1453 (t70) REVERT: A 582 ASP cc_start: 0.1473 (t0) cc_final: 0.1124 (t70) REVERT: A 592 ARG cc_start: -0.0135 (mmm160) cc_final: -0.1912 (ttm170) REVERT: B 37 ASN cc_start: 0.3720 (m-40) cc_final: 0.2674 (t0) REVERT: B 40 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.2376 (tp) REVERT: B 136 MET cc_start: 0.3131 (OUTLIER) cc_final: 0.0865 (mmm) REVERT: B 192 TRP cc_start: 0.0053 (m100) cc_final: -0.0472 (m100) REVERT: B 385 ILE cc_start: 0.3061 (mt) cc_final: 0.2727 (tp) REVERT: B 413 LYS cc_start: 0.2860 (OUTLIER) cc_final: 0.2282 (mmtt) REVERT: B 462 MET cc_start: 0.3112 (tpp) cc_final: -0.0075 (pmm) REVERT: B 487 MET cc_start: 0.3386 (mpp) cc_final: 0.2557 (mmt) REVERT: B 533 GLU cc_start: 0.3015 (OUTLIER) cc_final: 0.2491 (tp30) outliers start: 39 outliers final: 16 residues processed: 75 average time/residue: 0.9134 time to fit residues: 75.4447 Evaluate side-chains 59 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 101 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 236 ASN B 250 ASN B 396 GLN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.304890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.246342 restraints weight = 20470.576| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 5.75 r_work: 0.4342 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4344 r_free = 0.4344 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4344 r_free = 0.4344 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0502 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8987 Z= 0.285 Angle : 1.099 30.445 12219 Z= 0.512 Chirality : 0.055 0.350 1325 Planarity : 0.008 0.072 1590 Dihedral : 8.655 144.530 1274 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 5.49 % Allowed : 24.95 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1086 helix: 0.26 (0.27), residues: 387 sheet: -0.34 (0.41), residues: 162 loop : -1.28 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 348 HIS 0.011 0.002 HIS B 123 PHE 0.040 0.004 PHE A 161 TYR 0.046 0.003 TYR B 27 ARG 0.016 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.05596 ( 355) hydrogen bonds : angle 6.22492 ( 1006) metal coordination : bond 0.01278 ( 4) metal coordination : angle 12.37110 ( 12) covalent geometry : bond 0.00632 ( 8980) covalent geometry : angle 1.02867 (12207) Misc. bond : bond 0.02772 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 44 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.1355 (OUTLIER) cc_final: -0.1278 (p0) REVERT: A 540 TRP cc_start: 0.3187 (t-100) cc_final: 0.1396 (p90) REVERT: A 558 MET cc_start: 0.0450 (OUTLIER) cc_final: -0.1046 (tpp) REVERT: A 591 GLU cc_start: -0.0797 (OUTLIER) cc_final: -0.2150 (pm20) REVERT: B 19 GLU cc_start: 0.2582 (mm-30) cc_final: 0.2078 (tp30) REVERT: B 121 GLN cc_start: 0.3649 (OUTLIER) cc_final: 0.3148 (mt0) REVERT: B 136 MET cc_start: 0.3155 (OUTLIER) cc_final: 0.0866 (mmm) REVERT: B 209 GLN cc_start: -0.1418 (OUTLIER) cc_final: -0.1914 (mt0) REVERT: B 368 LEU cc_start: 0.1403 (OUTLIER) cc_final: 0.0163 (pp) REVERT: B 413 LYS cc_start: 0.3144 (OUTLIER) cc_final: 0.2477 (ptpt) REVERT: B 462 MET cc_start: 0.3221 (OUTLIER) cc_final: -0.0026 (pmm) REVERT: B 533 GLU cc_start: 0.3343 (OUTLIER) cc_final: 0.2450 (tp30) outliers start: 50 outliers final: 27 residues processed: 83 average time/residue: 1.0608 time to fit residues: 96.3659 Evaluate side-chains 75 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 38 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.307529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.262551 restraints weight = 28449.971| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 4.17 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4760 r_free = 0.4760 target_work(ls_wunit_k1) = 0.261 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4759 r_free = 0.4759 target_work(ls_wunit_k1) = 0.261 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0870 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8987 Z= 0.132 Angle : 0.799 27.624 12219 Z= 0.332 Chirality : 0.044 0.242 1325 Planarity : 0.005 0.067 1590 Dihedral : 7.602 139.758 1274 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 4.29 % Allowed : 26.15 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1086 helix: 0.64 (0.27), residues: 391 sheet: -0.59 (0.40), residues: 167 loop : -1.03 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.006 0.001 HIS B 123 PHE 0.024 0.002 PHE A 161 TYR 0.016 0.001 TYR B 27 ARG 0.005 0.001 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 355) hydrogen bonds : angle 5.26046 ( 1006) metal coordination : bond 0.00816 ( 4) metal coordination : angle 12.25891 ( 12) covalent geometry : bond 0.00288 ( 8980) covalent geometry : angle 0.70062 (12207) Misc. bond : bond 0.01429 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 40 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 444 ASN cc_start: 0.1018 (OUTLIER) cc_final: -0.0950 (p0) REVERT: A 471 MET cc_start: 0.3577 (tpp) cc_final: 0.3177 (tpp) REVERT: A 486 PHE cc_start: 0.0824 (m-80) cc_final: 0.0380 (m-10) REVERT: A 528 VAL cc_start: -0.0180 (OUTLIER) cc_final: -0.0730 (p) REVERT: A 558 MET cc_start: 0.0689 (OUTLIER) cc_final: -0.0243 (tpp) REVERT: A 591 GLU cc_start: 0.0937 (OUTLIER) cc_final: 0.0400 (mt-10) REVERT: B 37 ASN cc_start: 0.4885 (m-40) cc_final: 0.3831 (m110) REVERT: B 136 MET cc_start: 0.3597 (pp-130) cc_final: 0.1307 (mmm) REVERT: B 209 GLN cc_start: -0.0003 (OUTLIER) cc_final: -0.1231 (mt0) REVERT: B 368 LEU cc_start: 0.0606 (OUTLIER) cc_final: 0.0158 (pp) REVERT: B 373 ARG cc_start: -0.0711 (OUTLIER) cc_final: -0.2141 (mtm-85) REVERT: B 375 LEU cc_start: -0.0619 (OUTLIER) cc_final: -0.1371 (mt) REVERT: B 413 LYS cc_start: 0.2778 (OUTLIER) cc_final: 0.2071 (mmtt) REVERT: B 462 MET cc_start: 0.3104 (OUTLIER) cc_final: 0.0099 (pmm) outliers start: 39 outliers final: 20 residues processed: 71 average time/residue: 1.0002 time to fit residues: 77.6375 Evaluate side-chains 67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 37 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 HIS ** B 236 ASN ** 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 = 0.5114 r_free = 0.5114 target = 0.307896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.245550 restraints weight = 27263.151| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 8.05 r_work: 0.4282 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4277 r_free = 0.4277 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4277 r_free = 0.4277 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0339 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8987 Z= 0.131 Angle : 0.786 24.853 12219 Z= 0.329 Chirality : 0.043 0.190 1325 Planarity : 0.005 0.062 1590 Dihedral : 7.397 141.476 1274 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 4.18 % Allowed : 26.48 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1086 helix: 0.73 (0.27), residues: 393 sheet: -0.41 (0.41), residues: 161 loop : -0.99 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.006 0.001 HIS B 123 PHE 0.019 0.002 PHE A 161 TYR 0.012 0.001 TYR B 27 ARG 0.003 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 355) hydrogen bonds : angle 5.07561 ( 1006) metal coordination : bond 0.00702 ( 4) metal coordination : angle 11.67579 ( 12) covalent geometry : bond 0.00289 ( 8980) covalent geometry : angle 0.69605 (12207) Misc. bond : bond 0.01627 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0857 (OUTLIER) cc_final: -0.1192 (p0) REVERT: A 486 PHE cc_start: 0.1103 (m-80) cc_final: 0.0843 (m-10) REVERT: A 539 LEU cc_start: -0.0866 (OUTLIER) cc_final: -0.1265 (mt) REVERT: A 558 MET cc_start: 0.0492 (OUTLIER) cc_final: -0.0606 (tpp) REVERT: A 591 GLU cc_start: -0.1197 (OUTLIER) cc_final: -0.1490 (mt-10) REVERT: B 121 GLN cc_start: 0.2239 (OUTLIER) cc_final: 0.1856 (mt0) REVERT: B 125 ILE cc_start: -0.4643 (OUTLIER) cc_final: -0.5055 (mt) REVERT: B 136 MET cc_start: 0.3106 (pp-130) cc_final: 0.0775 (mmm) REVERT: B 209 GLN cc_start: -0.1926 (OUTLIER) cc_final: -0.2716 (mt0) REVERT: B 368 LEU cc_start: 0.0819 (OUTLIER) cc_final: 0.0105 (pp) REVERT: B 373 ARG cc_start: -0.1585 (OUTLIER) cc_final: -0.2591 (mtm-85) REVERT: B 375 LEU cc_start: -0.1927 (OUTLIER) cc_final: -0.2193 (mt) REVERT: B 413 LYS cc_start: 0.2762 (OUTLIER) cc_final: 0.2159 (mmtt) REVERT: B 448 GLU cc_start: -0.2025 (tt0) cc_final: -0.2440 (mt-10) REVERT: B 462 MET cc_start: 0.3082 (OUTLIER) cc_final: -0.0074 (pmm) REVERT: B 487 MET cc_start: 0.3486 (mpp) cc_final: 0.2582 (mmm) REVERT: B 533 GLU cc_start: 0.2885 (OUTLIER) cc_final: 0.1835 (tp30) outliers start: 38 outliers final: 20 residues processed: 71 average time/residue: 1.0173 time to fit residues: 78.8457 Evaluate side-chains 73 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 40 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.9980 chunk 99 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** 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 = 0.5120 r_free = 0.5120 target = 0.309078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.247435 restraints weight = 19882.252| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 5.10 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0386 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8987 Z= 0.125 Angle : 0.770 24.454 12219 Z= 0.318 Chirality : 0.043 0.166 1325 Planarity : 0.005 0.061 1590 Dihedral : 7.237 141.212 1274 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 4.29 % Allowed : 26.48 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1086 helix: 0.91 (0.27), residues: 394 sheet: -0.23 (0.41), residues: 164 loop : -0.93 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.006 0.001 HIS B 134 PHE 0.016 0.001 PHE A 161 TYR 0.011 0.001 TYR B 188 ARG 0.002 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 355) hydrogen bonds : angle 4.94450 ( 1006) metal coordination : bond 0.00611 ( 4) metal coordination : angle 11.63646 ( 12) covalent geometry : bond 0.00277 ( 8980) covalent geometry : angle 0.67808 (12207) Misc. bond : bond 0.01382 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 40 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0863 (OUTLIER) cc_final: -0.0989 (p0) REVERT: A 471 MET cc_start: 0.3285 (tpp) cc_final: 0.3040 (tpp) REVERT: A 486 PHE cc_start: 0.0736 (m-80) cc_final: 0.0392 (m-10) REVERT: A 539 LEU cc_start: -0.0637 (OUTLIER) cc_final: -0.1196 (mt) REVERT: A 558 MET cc_start: -0.0093 (OUTLIER) cc_final: -0.0956 (tpp) REVERT: A 591 GLU cc_start: -0.1401 (OUTLIER) cc_final: -0.1782 (mt-10) REVERT: B 121 GLN cc_start: 0.2016 (OUTLIER) cc_final: 0.1760 (mt0) REVERT: B 125 ILE cc_start: -0.4591 (OUTLIER) cc_final: -0.5011 (mt) REVERT: B 136 MET cc_start: 0.3203 (pp-130) cc_final: 0.0851 (mmm) REVERT: B 209 GLN cc_start: -0.1861 (OUTLIER) cc_final: -0.2627 (pm20) REVERT: B 368 LEU cc_start: 0.0670 (OUTLIER) cc_final: 0.0074 (pp) REVERT: B 373 ARG cc_start: -0.1382 (OUTLIER) cc_final: -0.2441 (mtm-85) REVERT: B 413 LYS cc_start: 0.2720 (OUTLIER) cc_final: 0.2220 (mmtt) REVERT: B 448 GLU cc_start: -0.1789 (tt0) cc_final: -0.2329 (mt-10) REVERT: B 462 MET cc_start: 0.3199 (OUTLIER) cc_final: 0.0194 (pmm) REVERT: B 487 MET cc_start: 0.3337 (mpp) cc_final: 0.2287 (mmt) REVERT: B 533 GLU cc_start: 0.3564 (OUTLIER) cc_final: 0.2282 (tp30) outliers start: 39 outliers final: 24 residues processed: 69 average time/residue: 1.1293 time to fit residues: 84.5635 Evaluate side-chains 76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 40 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.0970 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.310998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.253538 restraints weight = 21696.305| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 5.59 r_work: 0.4416 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0440 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8987 Z= 0.160 Angle : 0.845 24.609 12219 Z= 0.367 Chirality : 0.045 0.192 1325 Planarity : 0.006 0.059 1590 Dihedral : 7.497 141.206 1274 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 4.29 % Allowed : 26.37 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1086 helix: 0.64 (0.26), residues: 396 sheet: 0.03 (0.44), residues: 148 loop : -1.06 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.007 0.001 HIS B 134 PHE 0.027 0.002 PHE A 161 TYR 0.016 0.001 TYR A 527 ARG 0.006 0.001 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 355) hydrogen bonds : angle 5.20238 ( 1006) metal coordination : bond 0.00737 ( 4) metal coordination : angle 11.65136 ( 12) covalent geometry : bond 0.00353 ( 8980) covalent geometry : angle 0.76275 (12207) Misc. bond : bond 0.01719 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 38 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: -0.0027 (mt-10) cc_final: -0.0792 (mm-30) REVERT: A 444 ASN cc_start: 0.1051 (OUTLIER) cc_final: -0.1236 (p0) REVERT: A 486 PHE cc_start: 0.1041 (m-80) cc_final: 0.0737 (m-10) REVERT: A 532 LEU cc_start: 0.0436 (mp) cc_final: 0.0093 (mt) REVERT: A 539 LEU cc_start: -0.0596 (OUTLIER) cc_final: -0.1046 (mt) REVERT: A 591 GLU cc_start: -0.0954 (OUTLIER) cc_final: -0.2067 (mm-30) REVERT: B 37 ASN cc_start: 0.4109 (m-40) cc_final: 0.3526 (m110) REVERT: B 121 GLN cc_start: 0.2934 (OUTLIER) cc_final: 0.2470 (mt0) REVERT: B 125 ILE cc_start: -0.4366 (OUTLIER) cc_final: -0.4742 (tp) REVERT: B 136 MET cc_start: 0.3109 (pp-130) cc_final: 0.0855 (mmm) REVERT: B 209 GLN cc_start: -0.1326 (OUTLIER) cc_final: -0.2306 (mt0) REVERT: B 368 LEU cc_start: 0.1406 (OUTLIER) cc_final: 0.0073 (pp) REVERT: B 413 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2147 (ptpt) REVERT: B 462 MET cc_start: 0.3204 (OUTLIER) cc_final: -0.0023 (pmm) outliers start: 39 outliers final: 23 residues processed: 69 average time/residue: 1.0792 time to fit residues: 81.2167 Evaluate side-chains 67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 35 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** 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 = 0.5148 r_free = 0.5148 target = 0.312550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.256092 restraints weight = 28469.766| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 6.55 r_work: 0.4432 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0446 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8987 Z= 0.162 Angle : 0.851 25.537 12219 Z= 0.365 Chirality : 0.045 0.208 1325 Planarity : 0.006 0.062 1590 Dihedral : 7.521 139.705 1274 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.01 % Favored : 93.81 % Rotamer: Outliers : 4.07 % Allowed : 26.92 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1086 helix: 0.49 (0.26), residues: 400 sheet: -0.52 (0.41), residues: 164 loop : -0.98 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.007 0.001 HIS B 134 PHE 0.017 0.002 PHE B 120 TYR 0.015 0.001 TYR A 527 ARG 0.005 0.001 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 355) hydrogen bonds : angle 5.29046 ( 1006) metal coordination : bond 0.01535 ( 4) metal coordination : angle 11.83830 ( 12) covalent geometry : bond 0.00356 ( 8980) covalent geometry : angle 0.76602 (12207) Misc. bond : bond 0.03203 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 40 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0948 (OUTLIER) cc_final: -0.1081 (p0) REVERT: A 486 PHE cc_start: 0.1129 (m-80) cc_final: 0.0907 (m-10) REVERT: A 487 PHE cc_start: 0.1125 (t80) cc_final: 0.0840 (t80) REVERT: A 532 LEU cc_start: 0.0642 (mp) cc_final: 0.0423 (mt) REVERT: A 539 LEU cc_start: -0.0645 (OUTLIER) cc_final: -0.0912 (mt) REVERT: A 591 GLU cc_start: -0.1147 (OUTLIER) cc_final: -0.1485 (mt-10) REVERT: B 37 ASN cc_start: 0.4061 (m-40) cc_final: 0.3498 (m110) REVERT: B 121 GLN cc_start: 0.2731 (OUTLIER) cc_final: 0.2261 (mt0) REVERT: B 136 MET cc_start: 0.2840 (pp-130) cc_final: 0.0734 (mmm) REVERT: B 209 GLN cc_start: -0.0885 (OUTLIER) cc_final: -0.1957 (mt0) REVERT: B 413 LYS cc_start: 0.2744 (OUTLIER) cc_final: 0.2211 (ptpt) REVERT: B 432 MET cc_start: 0.5022 (mtm) cc_final: 0.4699 (pmm) REVERT: B 462 MET cc_start: 0.3282 (OUTLIER) cc_final: 0.0010 (pmm) outliers start: 37 outliers final: 25 residues processed: 69 average time/residue: 1.1396 time to fit residues: 85.5625 Evaluate side-chains 71 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 39 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** 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 = 0.5159 r_free = 0.5159 target = 0.314024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.259093 restraints weight = 22272.500| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 4.73 r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4670 r_free = 0.4670 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4670 r_free = 0.4670 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0552 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8987 Z= 0.152 Angle : 0.832 22.567 12219 Z= 0.357 Chirality : 0.045 0.181 1325 Planarity : 0.006 0.063 1590 Dihedral : 7.458 139.328 1274 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.01 % Favored : 93.81 % Rotamer: Outliers : 3.52 % Allowed : 27.47 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1086 helix: 0.57 (0.26), residues: 407 sheet: -0.51 (0.41), residues: 166 loop : -1.02 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.007 0.001 HIS B 134 PHE 0.016 0.002 PHE B 120 TYR 0.017 0.001 TYR A 527 ARG 0.007 0.001 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 355) hydrogen bonds : angle 5.21156 ( 1006) metal coordination : bond 0.01018 ( 4) metal coordination : angle 11.70622 ( 12) covalent geometry : bond 0.00335 ( 8980) covalent geometry : angle 0.74699 (12207) Misc. bond : bond 0.01858 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6980.14 seconds wall clock time: 120 minutes 24.43 seconds (7224.43 seconds total)