Starting phenix.real_space_refine on Mon May 12 07:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/05_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_45359/05_2025/9c91_45359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.map" model { file = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.33, per 1000 atoms: 0.83 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 1.5 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: 1.01 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: 2.47 Time building geometry restraints manager: 2.72 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: 3.090 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- 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 : 0.836 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: 0.8554 time to fit residues: 81.2167 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 : 0.944 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.211934 restraints weight = 20046.520| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 5.62 r_work: 0.3998 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0187 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 : 0.813 Fit side-chains REVERT: A 104 LYS cc_start: 0.0218 (OUTLIER) cc_final: -0.0268 (mtpt) REVERT: A 545 ASP cc_start: 0.1830 (m-30) cc_final: 0.1417 (t70) REVERT: A 582 ASP cc_start: 0.2221 (t0) cc_final: 0.1961 (t70) REVERT: A 591 GLU cc_start: -0.0637 (OUTLIER) cc_final: -0.1110 (tp30) REVERT: A 592 ARG cc_start: -0.0438 (mmm160) cc_final: -0.2262 (mtt90) REVERT: B 125 ILE cc_start: -0.4820 (OUTLIER) cc_final: -0.5593 (pp) REVERT: B 126 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.0388 (mm) REVERT: B 136 MET cc_start: 0.2905 (OUTLIER) cc_final: 0.0809 (mmm) REVERT: B 413 LYS cc_start: 0.2943 (OUTLIER) cc_final: 0.2387 (mmtt) REVERT: B 432 MET cc_start: 0.2866 (mtt) cc_final: 0.2658 (mmt) REVERT: B 533 GLU cc_start: 0.2619 (OUTLIER) cc_final: 0.2131 (tp30) outliers start: 47 outliers final: 14 residues processed: 89 average time/residue: 0.9154 time to fit residues: 89.2001 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 : 0.822 ------------------------------------------------------------------------------- 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: 0.0040 chunk 16 optimal weight: 30.0000 chunk 12 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- 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 = 0.5020 r_free = 0.5020 target = 0.295259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.247794 restraints weight = 24120.625| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 3.98 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4658 r_free = 0.4658 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4657 r_free = 0.4657 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0725 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8987 Z= 0.175 Angle : 0.845 25.650 12219 Z= 0.370 Chirality : 0.045 0.163 1325 Planarity : 0.006 0.053 1590 Dihedral : 7.585 137.520 1274 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % 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: -0.13 (0.26), residues: 1086 helix: 0.99 (0.27), residues: 392 sheet: -0.38 (0.38), residues: 182 loop : -0.76 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 484 HIS 0.006 0.001 HIS B 134 PHE 0.039 0.003 PHE A 486 TYR 0.019 0.002 TYR B 27 ARG 0.005 0.001 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 355) hydrogen bonds : angle 5.48506 ( 1006) metal coordination : bond 0.00960 ( 4) metal coordination : angle 11.37405 ( 12) covalent geometry : bond 0.00391 ( 8980) covalent geometry : angle 0.76693 (12207) Misc. bond : bond 0.02612 ( 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 80 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 41 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.0947 (OUTLIER) cc_final: 0.0699 (mm) REVERT: A 532 LEU cc_start: 0.0153 (OUTLIER) cc_final: -0.0383 (mp) REVERT: B 136 MET cc_start: 0.3270 (OUTLIER) cc_final: 0.1306 (mmm) REVERT: B 192 TRP cc_start: 0.2116 (m100) cc_final: 0.1291 (m100) REVERT: B 203 GLU cc_start: 0.2211 (OUTLIER) cc_final: 0.0329 (pt0) REVERT: B 413 LYS cc_start: 0.2681 (OUTLIER) cc_final: 0.2140 (mmtt) REVERT: B 487 MET cc_start: 0.3204 (mpp) cc_final: 0.2447 (mmm) outliers start: 39 outliers final: 19 residues processed: 73 average time/residue: 0.9473 time to fit residues: 75.9472 Evaluate side-chains 62 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE 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 379 LEU Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 0.0770 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 396 GLN B 504 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.301690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.229786 restraints weight = 16942.684| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 4.20 r_work: 0.4207 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0292 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8987 Z= 0.130 Angle : 0.771 24.165 12219 Z= 0.324 Chirality : 0.044 0.339 1325 Planarity : 0.005 0.057 1590 Dihedral : 7.489 143.899 1274 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 4.18 % Allowed : 24.62 % Favored : 71.21 % 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: 0.03 (0.26), residues: 1086 helix: 1.16 (0.27), residues: 393 sheet: -0.35 (0.38), residues: 184 loop : -0.70 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 484 HIS 0.006 0.001 HIS B 134 PHE 0.018 0.002 PHE A 486 TYR 0.017 0.001 TYR B 27 ARG 0.003 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 355) hydrogen bonds : angle 5.10579 ( 1006) metal coordination : bond 0.00754 ( 4) metal coordination : angle 11.54633 ( 12) covalent geometry : bond 0.00292 ( 8980) covalent geometry : angle 0.68146 (12207) Misc. bond : bond 0.01417 ( 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 79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0681 (OUTLIER) cc_final: -0.0579 (p0) REVERT: A 532 LEU cc_start: -0.0928 (OUTLIER) cc_final: -0.1454 (mt) REVERT: A 582 ASP cc_start: 0.1450 (t0) cc_final: 0.1076 (t70) REVERT: B 36 LEU cc_start: -0.2236 (OUTLIER) cc_final: -0.2591 (mp) REVERT: B 37 ASN cc_start: 0.3411 (m-40) cc_final: 0.2511 (t0) REVERT: B 136 MET cc_start: 0.3040 (OUTLIER) cc_final: 0.0831 (mmm) REVERT: B 192 TRP cc_start: -0.0013 (m100) cc_final: -0.0427 (m100) REVERT: B 413 LYS cc_start: 0.2862 (OUTLIER) cc_final: 0.2279 (mmtt) REVERT: B 462 MET cc_start: 0.2927 (tpp) cc_final: -0.0338 (pmm) REVERT: B 487 MET cc_start: 0.3401 (mpp) cc_final: 0.3115 (mtm) REVERT: B 533 GLU cc_start: 0.2842 (OUTLIER) cc_final: 0.2234 (tp30) outliers start: 38 outliers final: 18 residues processed: 72 average time/residue: 0.8144 time to fit residues: 65.1811 Evaluate side-chains 59 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 35 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 155 ASP 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 532 LEU Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 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: 10.0000 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.303948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.235242 restraints weight = 20935.130| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 5.78 r_work: 0.4231 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0324 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8987 Z= 0.154 Angle : 0.809 23.601 12219 Z= 0.348 Chirality : 0.044 0.357 1325 Planarity : 0.006 0.058 1590 Dihedral : 7.602 147.233 1274 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 4.51 % Allowed : 24.84 % Favored : 70.66 % 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: -0.22 (0.25), residues: 1086 helix: 0.98 (0.27), residues: 395 sheet: -0.60 (0.38), residues: 173 loop : -0.83 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 502 HIS 0.008 0.001 HIS B 123 PHE 0.018 0.002 PHE A 161 TYR 0.020 0.002 TYR B 27 ARG 0.005 0.001 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 355) hydrogen bonds : angle 5.12964 ( 1006) metal coordination : bond 0.00596 ( 4) metal coordination : angle 11.44368 ( 12) covalent geometry : bond 0.00345 ( 8980) covalent geometry : angle 0.72598 (12207) Misc. bond : bond 0.01381 ( 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 79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 38 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.0356 (OUTLIER) cc_final: -0.0435 (pm20) REVERT: A 174 GLU cc_start: -0.1674 (OUTLIER) cc_final: -0.2298 (mp0) REVERT: A 444 ASN cc_start: 0.0892 (OUTLIER) cc_final: -0.1661 (p0) REVERT: A 532 LEU cc_start: -0.0616 (OUTLIER) cc_final: -0.0923 (mt) REVERT: B 121 GLN cc_start: 0.2747 (OUTLIER) cc_final: 0.2366 (mt0) REVERT: B 136 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.0809 (mmm) REVERT: B 209 GLN cc_start: -0.2052 (OUTLIER) cc_final: -0.2320 (mp10) REVERT: B 413 LYS cc_start: 0.2800 (OUTLIER) cc_final: 0.2264 (mmtt) REVERT: B 462 MET cc_start: 0.2964 (OUTLIER) cc_final: -0.0312 (pmm) REVERT: B 487 MET cc_start: 0.3389 (mpp) cc_final: 0.3146 (mtm) REVERT: B 533 GLU cc_start: 0.2905 (OUTLIER) cc_final: 0.2233 (tp30) outliers start: 41 outliers final: 20 residues processed: 70 average time/residue: 0.9451 time to fit residues: 72.8164 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 174 GLU 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 532 LEU 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 126 LEU 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 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 221 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 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 = 0.5121 r_free = 0.5121 target = 0.307806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.261404 restraints weight = 28678.660| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 4.40 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4741 r_free = 0.4741 target_work(ls_wunit_k1) = 0.258 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4741 r_free = 0.4741 target_work(ls_wunit_k1) = 0.258 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0797 moved from start: 0.5699 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= 0.135 Angle : 0.781 23.673 12219 Z= 0.327 Chirality : 0.044 0.256 1325 Planarity : 0.005 0.061 1590 Dihedral : 7.379 142.531 1274 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 4.18 % Allowed : 25.05 % Favored : 70.77 % 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: -0.14 (0.26), residues: 1086 helix: 1.00 (0.27), residues: 396 sheet: -0.46 (0.40), residues: 173 loop : -0.77 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.009 0.001 HIS B 123 PHE 0.018 0.002 PHE A 161 TYR 0.017 0.001 TYR B 27 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 355) hydrogen bonds : angle 4.93739 ( 1006) metal coordination : bond 0.00659 ( 4) metal coordination : angle 11.81662 ( 12) covalent geometry : bond 0.00301 ( 8980) covalent geometry : angle 0.68802 (12207) Misc. bond : bond 0.01416 ( 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 78 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 40 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0905 (OUTLIER) cc_final: -0.0811 (p0) REVERT: A 471 MET cc_start: 0.3562 (tpp) cc_final: 0.3205 (tpp) REVERT: A 486 PHE cc_start: 0.0668 (m-80) cc_final: 0.0222 (m-10) REVERT: A 528 VAL cc_start: -0.0241 (OUTLIER) cc_final: -0.0681 (p) REVERT: A 532 LEU cc_start: 0.0839 (OUTLIER) cc_final: 0.0017 (mt) REVERT: A 558 MET cc_start: 0.0909 (OUTLIER) cc_final: -0.0022 (tpp) REVERT: B 37 ASN cc_start: 0.4528 (m-40) cc_final: 0.3090 (t0) REVERT: B 121 GLN cc_start: 0.3147 (OUTLIER) cc_final: 0.2904 (mt0) REVERT: B 136 MET cc_start: 0.3634 (pp-130) cc_final: 0.1446 (mmm) REVERT: B 209 GLN cc_start: -0.0406 (OUTLIER) cc_final: -0.1253 (mp10) REVERT: B 375 LEU cc_start: -0.0592 (OUTLIER) cc_final: -0.1353 (mt) REVERT: B 413 LYS cc_start: 0.2526 (OUTLIER) cc_final: 0.2048 (mmtt) REVERT: B 462 MET cc_start: 0.3188 (OUTLIER) cc_final: 0.0144 (pmm) REVERT: B 487 MET cc_start: 0.3056 (mpp) cc_final: 0.2519 (mtm) REVERT: B 533 GLU cc_start: 0.3235 (OUTLIER) cc_final: 0.2530 (tp30) outliers start: 38 outliers final: 16 residues processed: 72 average time/residue: 0.9337 time to fit residues: 74.3204 Evaluate side-chains 66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 532 LEU Chi-restraints excluded: chain A residue 558 MET 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 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL 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 Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.0980 chunk 51 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 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 = 0.5117 r_free = 0.5117 target = 0.307777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.244184 restraints weight = 26978.600| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 7.59 r_work: 0.4285 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4283 r_free = 0.4283 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4283 r_free = 0.4283 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.4283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0330 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8987 Z= 0.128 Angle : 0.759 22.827 12219 Z= 0.318 Chirality : 0.043 0.207 1325 Planarity : 0.005 0.060 1590 Dihedral : 7.287 143.195 1274 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 3.41 % Allowed : 25.93 % Favored : 70.66 % 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: -0.09 (0.26), residues: 1086 helix: 1.05 (0.27), residues: 396 sheet: -0.50 (0.38), residues: 183 loop : -0.72 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.008 0.001 HIS A 548 PHE 0.016 0.002 PHE A 161 TYR 0.017 0.001 TYR B 370 ARG 0.006 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 355) hydrogen bonds : angle 4.82853 ( 1006) metal coordination : bond 0.00633 ( 4) metal coordination : angle 11.46532 ( 12) covalent geometry : bond 0.00285 ( 8980) covalent geometry : angle 0.66904 (12207) Misc. bond : bond 0.01329 ( 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 73 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0706 (OUTLIER) cc_final: -0.1137 (p0) REVERT: A 532 LEU cc_start: -0.0421 (OUTLIER) cc_final: -0.0925 (mp) REVERT: A 539 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.1022 (mt) REVERT: A 558 MET cc_start: 0.0582 (OUTLIER) cc_final: -0.0860 (tpp) REVERT: B 62 ASP cc_start: -0.1369 (m-30) cc_final: -0.1623 (t0) REVERT: B 121 GLN cc_start: 0.2318 (OUTLIER) cc_final: 0.1909 (mt0) REVERT: B 136 MET cc_start: 0.3193 (pp-130) cc_final: 0.0889 (mmm) REVERT: B 209 GLN cc_start: -0.1985 (OUTLIER) cc_final: -0.2309 (mt0) REVERT: B 211 TYR cc_start: 0.1114 (m-80) cc_final: 0.0501 (t80) REVERT: B 373 ARG cc_start: -0.1495 (OUTLIER) cc_final: -0.2514 (mmm-85) REVERT: B 375 LEU cc_start: -0.1739 (OUTLIER) cc_final: -0.2061 (mt) REVERT: B 413 LYS cc_start: 0.2750 (OUTLIER) cc_final: 0.2249 (mmtt) REVERT: B 462 MET cc_start: 0.3158 (OUTLIER) cc_final: -0.0046 (pmm) REVERT: B 487 MET cc_start: 0.3296 (mpp) cc_final: 0.3002 (mtm) outliers start: 31 outliers final: 17 residues processed: 67 average time/residue: 1.0898 time to fit residues: 79.6805 Evaluate side-chains 66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 135 LEU 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 532 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET 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 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 279 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 55 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.309001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.246334 restraints weight = 19650.550| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 4.92 r_work: 0.4332 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0320 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8987 Z= 0.120 Angle : 0.749 22.584 12219 Z= 0.308 Chirality : 0.043 0.183 1325 Planarity : 0.005 0.060 1590 Dihedral : 7.162 142.702 1274 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 3.41 % Allowed : 26.15 % Favored : 70.44 % 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: 0.03 (0.26), residues: 1086 helix: 1.16 (0.27), residues: 396 sheet: -0.40 (0.39), residues: 188 loop : -0.67 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 348 HIS 0.007 0.001 HIS B 134 PHE 0.014 0.001 PHE A 161 TYR 0.013 0.001 TYR B 188 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 355) hydrogen bonds : angle 4.71117 ( 1006) metal coordination : bond 0.00559 ( 4) metal coordination : angle 11.51463 ( 12) covalent geometry : bond 0.00268 ( 8980) covalent geometry : angle 0.65682 (12207) Misc. bond : bond 0.01218 ( 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 72 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 41 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0671 (OUTLIER) cc_final: -0.1011 (p0) REVERT: A 532 LEU cc_start: -0.0322 (OUTLIER) cc_final: -0.0725 (mt) REVERT: A 539 LEU cc_start: -0.0689 (OUTLIER) cc_final: -0.1035 (mt) REVERT: A 558 MET cc_start: 0.0502 (OUTLIER) cc_final: -0.0852 (tpp) REVERT: B 62 ASP cc_start: -0.1438 (OUTLIER) cc_final: -0.1820 (t0) REVERT: B 136 MET cc_start: 0.3096 (pp-130) cc_final: 0.0894 (mmm) REVERT: B 209 GLN cc_start: -0.1941 (OUTLIER) cc_final: -0.2598 (mt0) REVERT: B 211 TYR cc_start: 0.0956 (m-80) cc_final: 0.0410 (t80) REVERT: B 370 TYR cc_start: 0.2269 (m-10) cc_final: 0.2017 (OUTLIER) REVERT: B 373 ARG cc_start: -0.1417 (OUTLIER) cc_final: -0.2699 (mmm-85) REVERT: B 413 LYS cc_start: 0.2581 (OUTLIER) cc_final: 0.2108 (mmtt) REVERT: B 462 MET cc_start: 0.3066 (OUTLIER) cc_final: -0.0138 (pmm) REVERT: B 487 MET cc_start: 0.3257 (mpp) cc_final: 0.2948 (mtm) outliers start: 31 outliers final: 18 residues processed: 63 average time/residue: 1.0251 time to fit residues: 70.6386 Evaluate side-chains 65 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain A residue 168 PHE 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 532 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET 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 62 ASP 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 196 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.310906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.249047 restraints weight = 21723.074| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 6.37 r_work: 0.4344 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4321 r_free = 0.4321 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4321 r_free = 0.4321 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0317 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8987 Z= 0.123 Angle : 0.763 22.310 12219 Z= 0.318 Chirality : 0.043 0.175 1325 Planarity : 0.005 0.065 1590 Dihedral : 7.152 142.233 1274 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 3.30 % Allowed : 27.03 % 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: 0.06 (0.26), residues: 1086 helix: 1.19 (0.27), residues: 397 sheet: -0.32 (0.40), residues: 183 loop : -0.69 (0.27), residues: 506 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 0.013 0.001 PHE A 161 TYR 0.012 0.001 TYR B 188 ARG 0.009 0.000 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 355) hydrogen bonds : angle 4.68129 ( 1006) metal coordination : bond 0.00567 ( 4) metal coordination : angle 11.22147 ( 12) covalent geometry : bond 0.00275 ( 8980) covalent geometry : angle 0.67779 (12207) Misc. bond : bond 0.01139 ( 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 69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0572 (OUTLIER) cc_final: -0.1124 (p0) REVERT: A 532 LEU cc_start: -0.0255 (OUTLIER) cc_final: -0.0610 (mt) REVERT: A 539 LEU cc_start: -0.0715 (OUTLIER) cc_final: -0.0975 (mt) REVERT: A 558 MET cc_start: 0.0344 (OUTLIER) cc_final: -0.0916 (tpp) REVERT: B 20 ARG cc_start: 0.2522 (tmm160) cc_final: 0.1443 (tmt170) REVERT: B 136 MET cc_start: 0.3094 (pp-130) cc_final: 0.0878 (mmm) REVERT: B 209 GLN cc_start: -0.1862 (OUTLIER) cc_final: -0.2531 (mt0) REVERT: B 211 TYR cc_start: 0.1008 (m-80) cc_final: 0.0336 (t80) REVERT: B 413 LYS cc_start: 0.2571 (OUTLIER) cc_final: 0.2121 (mmtt) REVERT: B 462 MET cc_start: 0.3230 (OUTLIER) cc_final: -0.0077 (pmm) REVERT: B 487 MET cc_start: 0.3294 (mpp) cc_final: 0.2991 (mtm) outliers start: 30 outliers final: 21 residues processed: 61 average time/residue: 1.0297 time to fit residues: 68.7288 Evaluate side-chains 66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 135 LEU 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 532 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET 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 100 ASP 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 196 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.310718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.251725 restraints weight = 28227.107| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 7.62 r_work: 0.4326 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4331 r_free = 0.4331 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4331 r_free = 0.4331 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0336 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8987 Z= 0.128 Angle : 0.767 22.104 12219 Z= 0.322 Chirality : 0.043 0.190 1325 Planarity : 0.005 0.060 1590 Dihedral : 7.176 141.965 1274 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 3.08 % Allowed : 27.14 % Favored : 69.78 % 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: 0.04 (0.26), residues: 1086 helix: 1.14 (0.27), residues: 398 sheet: -0.31 (0.40), residues: 183 loop : -0.69 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 542 HIS 0.006 0.001 HIS B 134 PHE 0.015 0.001 PHE A 161 TYR 0.014 0.001 TYR A 527 ARG 0.009 0.000 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 355) hydrogen bonds : angle 4.72478 ( 1006) metal coordination : bond 0.00631 ( 4) metal coordination : angle 11.10013 ( 12) covalent geometry : bond 0.00285 ( 8980) covalent geometry : angle 0.68437 (12207) Misc. bond : bond 0.01306 ( 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 67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0605 (OUTLIER) cc_final: -0.1163 (p0) REVERT: A 532 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0499 (mt) REVERT: A 539 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.0878 (mt) REVERT: A 558 MET cc_start: 0.0331 (OUTLIER) cc_final: -0.0872 (tpp) REVERT: B 20 ARG cc_start: 0.2513 (tmm160) cc_final: 0.1434 (tmt170) REVERT: B 121 GLN cc_start: 0.2178 (OUTLIER) cc_final: 0.1716 (mt0) REVERT: B 136 MET cc_start: 0.3114 (pp-130) cc_final: 0.0878 (mmm) REVERT: B 209 GLN cc_start: -0.1792 (OUTLIER) cc_final: -0.2293 (mt0) REVERT: B 211 TYR cc_start: 0.1050 (m-80) cc_final: 0.0303 (t80) REVERT: B 413 LYS cc_start: 0.2550 (OUTLIER) cc_final: 0.2098 (mmtt) REVERT: B 462 MET cc_start: 0.3159 (OUTLIER) cc_final: -0.0155 (pmm) REVERT: B 487 MET cc_start: 0.3302 (mpp) cc_final: 0.2999 (mtm) outliers start: 28 outliers final: 20 residues processed: 59 average time/residue: 1.0115 time to fit residues: 65.6148 Evaluate side-chains 67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 135 LEU 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 532 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 MET 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 100 ASP Chi-restraints excluded: chain B residue 121 GLN 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 196 GLU 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 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 19 optimal weight: 0.0030 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 33 optimal weight: 0.0050 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 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 = 0.5147 r_free = 0.5147 target = 0.311462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.249319 restraints weight = 22149.039| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 5.54 r_work: 0.4356 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.4356 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4344 r_free = 0.4344 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0305 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8987 Z= 0.110 Angle : 0.732 21.386 12219 Z= 0.299 Chirality : 0.042 0.177 1325 Planarity : 0.005 0.061 1590 Dihedral : 7.013 142.653 1274 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 2.20 % Allowed : 28.13 % 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: 0.23 (0.26), residues: 1086 helix: 1.34 (0.27), residues: 399 sheet: -0.31 (0.40), residues: 183 loop : -0.58 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.008 0.001 HIS B 134 PHE 0.012 0.001 PHE A 161 TYR 0.012 0.001 TYR B 188 ARG 0.008 0.000 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 355) hydrogen bonds : angle 4.55713 ( 1006) metal coordination : bond 0.00418 ( 4) metal coordination : angle 11.28388 ( 12) covalent geometry : bond 0.00246 ( 8980) covalent geometry : angle 0.64088 (12207) Misc. bond : bond 0.00775 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6788.49 seconds wall clock time: 117 minutes 29.84 seconds (7049.84 seconds total)