Starting phenix.real_space_refine on Thu Jul 2 13:08:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_45359.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_45359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_45359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_45359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/07_2026/9c91_45359.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 76 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'PO4': 1, 'SF4': 1, 'SRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 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: 2.15, per 1000 atoms: 0.24 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: 0.77 Conformation dependent library (CDL) restraints added in 291.1 milliseconds 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: 0.23 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: 1.37 Time building geometry restraints manager: 0.91 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: 4.180 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0033 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 : 10.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (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 ARG 0.005 0.000 ARG B 29 TYR 0.019 0.001 TYR A 332 PHE 0.016 0.002 PHE A 103 TRP 0.015 0.001 TRP A 295 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 8980) covalent geometry : angle 0.69069 / 0.32 (12207) hydrogen bonds : bond 0.16652 / 10.06 ( 355) hydrogen bonds : angle 6.99197 / 4.80 ( 1006) metal coordination : bond 0.01592 / 0.74 ( 4) metal coordination : angle 9.90915 / 5.41 ( 12) Misc. bond : bond 0.02842 / 1.06 ( 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 : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ILE cc_start: -0.0196 (mt) cc_final: -0.1598 (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: 0.3218 time to fit residues: 30.6178 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 : 0.221 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 40.0000 chunk 100 optimal weight: 0.0000 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.294008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.241972 restraints weight = 26264.869| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 4.41 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0480 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8987 Z= 0.177 Angle : 0.851 19.153 12219 Z= 0.378 Chirality : 0.047 0.197 1325 Planarity : 0.006 0.049 1590 Dihedral : 7.562 139.162 1281 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 5.05 % Allowed : 25.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1086 helix: 1.24 (0.27), residues: 392 sheet: -0.35 (0.36), residues: 200 loop : -0.65 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 596 TYR 0.019 0.002 TYR A 527 PHE 0.022 0.003 PHE B 122 TRP 0.024 0.002 TRP A 542 HIS 0.010 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 8980) covalent geometry : angle 0.77012 / 0.38 (12207) hydrogen bonds : bond 0.04139 / 2.72 ( 355) hydrogen bonds : angle 5.62445 / 3.93 ( 1006) metal coordination : bond 0.01470 / 0.65 ( 4) metal coordination : angle 11.61658 / 6.34 ( 12) Misc. bond : bond 0.01134 / 0.43 ( 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 92 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 46 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.0502 (OUTLIER) cc_final: -0.0266 (mtpt) REVERT: A 110 LYS cc_start: 0.1972 (mmtt) cc_final: 0.1440 (tppt) REVERT: A 181 LEU cc_start: 0.1218 (tm) cc_final: 0.0991 (tt) REVERT: A 582 ASP cc_start: 0.3634 (t0) cc_final: 0.3147 (t70) REVERT: A 591 GLU cc_start: -0.0250 (OUTLIER) cc_final: -0.0767 (tp30) REVERT: A 592 ARG cc_start: 0.1126 (mmm160) cc_final: -0.1186 (ttm170) REVERT: B 135 GLN cc_start: 0.1451 (mm110) cc_final: -0.0592 (pt0) REVERT: B 136 MET cc_start: 0.3266 (OUTLIER) cc_final: 0.1209 (mmm) REVERT: B 413 LYS cc_start: 0.2567 (OUTLIER) cc_final: 0.2095 (mmtt) REVERT: B 432 MET cc_start: 0.2653 (mtt) cc_final: 0.2439 (mtt) REVERT: B 485 ARG cc_start: -0.0128 (mtm-85) cc_final: -0.1338 (mtt180) REVERT: B 487 MET cc_start: 0.3268 (mpp) cc_final: 0.2530 (mmt) REVERT: B 533 GLU cc_start: 0.2460 (OUTLIER) cc_final: 0.2049 (tp30) outliers start: 46 outliers final: 14 residues processed: 87 average time/residue: 0.3670 time to fit residues: 34.8356 Evaluate side-chains 60 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN B 129 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 250 ASN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.295297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.246700 restraints weight = 24312.228| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 3.99 r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4634 r_free = 0.4634 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4633 r_free = 0.4633 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0767 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8987 Z= 0.204 Angle : 0.903 27.378 12219 Z= 0.404 Chirality : 0.047 0.187 1325 Planarity : 0.007 0.060 1590 Dihedral : 7.857 137.951 1274 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.95 % Allowed : 24.73 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1086 helix: 0.88 (0.27), residues: 389 sheet: -0.27 (0.40), residues: 170 loop : -0.94 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 485 TYR 0.024 0.002 TYR B 27 PHE 0.051 0.003 PHE A 486 TRP 0.015 0.002 TRP A 484 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 8980) covalent geometry : angle 0.82810 / 0.40 (12207) hydrogen bonds : bond 0.04368 / 2.94 ( 355) hydrogen bonds : angle 5.70110 / 4.00 ( 1006) metal coordination : bond 0.01123 / 0.53 ( 4) metal coordination : angle 11.52744 / 6.58 ( 12) Misc. bond : bond 0.03193 / 1.19 ( 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 90 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 45 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.2220 (mmtt) cc_final: 0.1591 (tppt) REVERT: A 127 GLU cc_start: 0.0528 (OUTLIER) cc_final: -0.0882 (pm20) REVERT: A 379 LEU cc_start: 0.0912 (OUTLIER) cc_final: 0.0663 (mm) REVERT: A 444 ASN cc_start: 0.1422 (OUTLIER) cc_final: -0.0768 (p0) REVERT: A 532 LEU cc_start: 0.0304 (OUTLIER) cc_final: -0.0340 (mp) REVERT: B 40 LEU cc_start: 0.2611 (OUTLIER) cc_final: 0.2378 (tp) REVERT: B 125 ILE cc_start: -0.2353 (OUTLIER) cc_final: -0.3580 (tp) REVERT: B 136 MET cc_start: 0.3297 (OUTLIER) cc_final: 0.1316 (mmm) REVERT: B 192 TRP cc_start: 0.2317 (m100) cc_final: 0.1313 (m100) REVERT: B 203 GLU cc_start: 0.2253 (OUTLIER) cc_final: 0.0484 (pt0) REVERT: B 413 LYS cc_start: 0.2814 (OUTLIER) cc_final: 0.2197 (mmtt) REVERT: B 462 MET cc_start: 0.2849 (tpp) cc_final: -0.0255 (pmm) REVERT: B 533 GLU cc_start: 0.2864 (OUTLIER) cc_final: 0.2249 (tp30) outliers start: 45 outliers final: 25 residues processed: 83 average time/residue: 0.4015 time to fit residues: 36.3367 Evaluate side-chains 75 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 40 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 135 LEU 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 379 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.1980 chunk 89 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 0.0470 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS B 395 ASN B 396 GLN B 504 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.303033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.256029 restraints weight = 30118.583| |-----------------------------------------------------------------------------| r_work (start): 0.4699 rms_B_bonded: 4.54 r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4714 r_free = 0.4714 target_work(ls_wunit_k1) = 0.256 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4714 r_free = 0.4714 target_work(ls_wunit_k1) = 0.256 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0829 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8987 Z= 0.176 Angle : 0.844 29.497 12219 Z= 0.371 Chirality : 0.045 0.166 1325 Planarity : 0.006 0.060 1590 Dihedral : 7.817 144.238 1274 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 5.16 % Allowed : 25.38 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1086 helix: 0.74 (0.27), residues: 392 sheet: -0.24 (0.41), residues: 170 loop : -0.95 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 557 TYR 0.031 0.002 TYR B 27 PHE 0.027 0.003 PHE A 486 TRP 0.010 0.001 TRP A 197 HIS 0.008 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8980) covalent geometry : angle 0.76077 / 0.37 (12207) hydrogen bonds : bond 0.03967 / 2.66 ( 355) hydrogen bonds : angle 5.39850 / 3.73 ( 1006) metal coordination : bond 0.01711 / 0.83 ( 4) metal coordination : angle 11.71223 / 6.61 ( 12) Misc. bond : bond 0.03827 / 1.42 ( 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 93 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 46 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.1621 (OUTLIER) cc_final: 0.1313 (ptpt) REVERT: A 110 LYS cc_start: 0.1864 (mmtt) cc_final: 0.1371 (tppt) REVERT: A 112 LEU cc_start: 0.0716 (pp) cc_final: 0.0489 (mm) REVERT: A 168 PHE cc_start: 0.1791 (OUTLIER) cc_final: 0.1284 (m-80) REVERT: A 174 GLU cc_start: 0.0358 (OUTLIER) cc_final: -0.0403 (tp30) REVERT: A 379 LEU cc_start: 0.0987 (OUTLIER) cc_final: 0.0776 (mm) REVERT: A 532 LEU cc_start: 0.0892 (OUTLIER) cc_final: -0.0004 (mt) REVERT: B 36 LEU cc_start: 0.0606 (OUTLIER) cc_final: 0.0224 (tp) REVERT: B 37 ASN cc_start: 0.4721 (OUTLIER) cc_final: 0.2960 (t0) REVERT: B 121 GLN cc_start: 0.3506 (OUTLIER) cc_final: 0.3267 (mt0) REVERT: B 125 ILE cc_start: -0.2708 (OUTLIER) cc_final: -0.4467 (pp) REVERT: B 136 MET cc_start: 0.3556 (OUTLIER) cc_final: 0.1362 (mmm) REVERT: B 209 GLN cc_start: -0.0563 (OUTLIER) cc_final: -0.1211 (mp10) REVERT: B 373 ARG cc_start: -0.0918 (OUTLIER) cc_final: -0.1571 (ttm110) REVERT: B 375 LEU cc_start: -0.0461 (OUTLIER) cc_final: -0.1215 (mt) REVERT: B 413 LYS cc_start: 0.2883 (OUTLIER) cc_final: 0.2181 (mmtt) REVERT: B 462 MET cc_start: 0.2917 (OUTLIER) cc_final: -0.0202 (pmm) REVERT: B 487 MET cc_start: 0.1199 (mpp) cc_final: 0.0697 (mpp) REVERT: B 533 GLU cc_start: 0.3102 (OUTLIER) cc_final: 0.2326 (tp30) outliers start: 47 outliers final: 18 residues processed: 80 average time/residue: 0.4083 time to fit residues: 35.4852 Evaluate side-chains 76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 42 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 104 LYS 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 297 LYS 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 532 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 375 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 105 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.304965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.257606 restraints weight = 28378.915| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 4.31 r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4718 r_free = 0.4718 target_work(ls_wunit_k1) = 0.256 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4718 r_free = 0.4718 target_work(ls_wunit_k1) = 0.256 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0733 moved from start: 0.5223 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= 0.127 Angle : 0.764 26.070 12219 Z= 0.316 Chirality : 0.042 0.152 1325 Planarity : 0.005 0.059 1590 Dihedral : 7.517 152.084 1274 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 3.63 % Allowed : 26.48 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1086 helix: 1.00 (0.27), residues: 394 sheet: -0.45 (0.37), residues: 195 loop : -0.78 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.017 0.001 TYR B 27 PHE 0.017 0.001 PHE A 161 TRP 0.006 0.001 TRP A 197 HIS 0.006 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8980) covalent geometry : angle 0.67016 / 0.32 (12207) hydrogen bonds : bond 0.03290 / 2.17 ( 355) hydrogen bonds : angle 5.05632 / 3.50 ( 1006) metal coordination : bond 0.00826 / 0.40 ( 4) metal coordination : angle 11.75693 / 6.59 ( 12) Misc. bond : bond 0.01561 / 0.59 ( 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 78 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.1092 (mmtt) cc_final: 0.0802 (tppt) REVERT: A 112 LEU cc_start: 0.0641 (OUTLIER) cc_final: 0.0439 (mt) REVERT: A 379 LEU cc_start: 0.0928 (OUTLIER) cc_final: 0.0716 (mm) REVERT: A 532 LEU cc_start: 0.0707 (OUTLIER) cc_final: -0.0025 (mt) REVERT: A 557 ARG cc_start: 0.1613 (tpm170) cc_final: 0.1350 (tpm170) REVERT: A 558 MET cc_start: 0.0878 (OUTLIER) cc_final: -0.0158 (tpp) REVERT: B 36 LEU cc_start: 0.0225 (OUTLIER) cc_final: -0.0210 (tp) REVERT: B 37 ASN cc_start: 0.4344 (m-40) cc_final: 0.3041 (t0) REVERT: B 136 MET cc_start: 0.3532 (pp-130) cc_final: 0.1323 (mmm) REVERT: B 209 GLN cc_start: -0.0840 (OUTLIER) cc_final: -0.1370 (mp10) REVERT: B 413 LYS cc_start: 0.2734 (OUTLIER) cc_final: 0.2206 (mmtt) REVERT: B 462 MET cc_start: 0.3085 (OUTLIER) cc_final: 0.0011 (pmm) REVERT: B 487 MET cc_start: 0.1046 (mpp) cc_final: 0.0588 (mpp) outliers start: 33 outliers final: 16 residues processed: 70 average time/residue: 0.3719 time to fit residues: 28.2684 Evaluate side-chains 66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 112 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 379 LEU 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 36 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 125 ILE 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 209 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.307474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.238975 restraints weight = 23692.615| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 7.05 r_work: 0.4255 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.4274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0306 moved from start: 0.5786 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= 0.141 Angle : 0.790 20.743 12219 Z= 0.336 Chirality : 0.043 0.156 1325 Planarity : 0.005 0.058 1590 Dihedral : 7.466 147.989 1274 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 5.05 % Allowed : 25.05 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1086 helix: 1.00 (0.27), residues: 393 sheet: -0.40 (0.38), residues: 188 loop : -0.74 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.021 0.002 TYR B 27 PHE 0.017 0.002 PHE A 161 TRP 0.007 0.001 TRP A 197 HIS 0.007 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8980) covalent geometry : angle 0.71020 / 0.34 (12207) hydrogen bonds : bond 0.03503 / 2.32 ( 355) hydrogen bonds : angle 5.02131 / 3.46 ( 1006) metal coordination : bond 0.00601 / 0.28 ( 4) metal coordination : angle 11.06190 / 6.01 ( 12) Misc. bond : bond 0.00762 / 0.30 ( 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 89 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 43 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.0594 (OUTLIER) cc_final: -0.1497 (p0) REVERT: A 558 MET cc_start: 0.0641 (OUTLIER) cc_final: -0.0411 (tpp) REVERT: B 121 GLN cc_start: 0.2221 (OUTLIER) cc_final: 0.1793 (mt0) REVERT: B 125 ILE cc_start: -0.4744 (OUTLIER) cc_final: -0.5041 (tp) REVERT: B 136 MET cc_start: 0.2893 (OUTLIER) cc_final: 0.0855 (mmm) REVERT: B 202 ASP cc_start: 0.3872 (m-30) cc_final: 0.3529 (m-30) REVERT: B 209 GLN cc_start: -0.1764 (OUTLIER) cc_final: -0.2564 (mp-120) REVERT: B 373 ARG cc_start: -0.1805 (OUTLIER) cc_final: -0.2760 (mmm-85) REVERT: B 375 LEU cc_start: -0.1670 (OUTLIER) cc_final: -0.1995 (mt) REVERT: B 413 LYS cc_start: 0.2790 (OUTLIER) cc_final: 0.2270 (mmtt) REVERT: B 462 MET cc_start: 0.3100 (OUTLIER) cc_final: -0.0108 (pmm) REVERT: B 487 MET cc_start: 0.2082 (mpp) cc_final: 0.1625 (mpp) outliers start: 46 outliers final: 23 residues processed: 79 average time/residue: 0.3678 time to fit residues: 31.6367 Evaluate side-chains 73 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 40 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 LYS 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 125 ILE Chi-restraints excluded: chain B residue 128 LYS 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 166 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 209 GLN 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 420 LEU Chi-restraints excluded: chain B residue 462 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN 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 = 0.308698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.244153 restraints weight = 21760.795| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 5.88 r_work: 0.4288 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4288 r_free = 0.4288 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4288 r_free = 0.4288 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0317 moved from start: 0.5976 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= 0.121 Angle : 0.750 23.091 12219 Z= 0.309 Chirality : 0.043 0.155 1325 Planarity : 0.005 0.059 1590 Dihedral : 7.264 147.557 1274 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 3.96 % Allowed : 25.82 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1086 helix: 1.10 (0.27), residues: 395 sheet: -0.34 (0.38), residues: 195 loop : -0.72 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.014 0.001 TYR B 27 PHE 0.031 0.002 PHE A 148 TRP 0.005 0.001 TRP A 542 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8980) covalent geometry : angle 0.66045 / 0.31 (12207) hydrogen bonds : bond 0.02994 / 1.99 ( 355) hydrogen bonds : angle 4.79392 / 3.31 ( 1006) metal coordination : bond 0.00603 / 0.29 ( 4) metal coordination : angle 11.36553 / 6.34 ( 12) Misc. bond : bond 0.01187 / 0.45 ( 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 77 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: -0.0066 (mt-10) cc_final: -0.1304 (tp30) REVERT: A 444 ASN cc_start: 0.0492 (OUTLIER) cc_final: -0.1342 (p0) REVERT: A 558 MET cc_start: 0.0633 (OUTLIER) cc_final: -0.0427 (tpp) REVERT: B 37 ASN cc_start: 0.3677 (m-40) cc_final: 0.2883 (t0) REVERT: B 45 LYS cc_start: 0.3825 (OUTLIER) cc_final: 0.1786 (mtmm) REVERT: B 125 ILE cc_start: -0.4568 (OUTLIER) cc_final: -0.5017 (mt) REVERT: B 136 MET cc_start: 0.3116 (pp-130) cc_final: 0.0862 (mmm) REVERT: B 166 LEU cc_start: 0.1510 (OUTLIER) cc_final: 0.0853 (tm) REVERT: B 186 ARG cc_start: 0.0817 (mtt180) cc_final: -0.0268 (mmt180) REVERT: B 209 GLN cc_start: -0.2059 (OUTLIER) cc_final: -0.3073 (pm20) REVERT: B 373 ARG cc_start: -0.1303 (OUTLIER) cc_final: -0.2276 (mmm-85) REVERT: B 413 LYS cc_start: 0.2833 (OUTLIER) cc_final: 0.2294 (mmtt) REVERT: B 462 MET cc_start: 0.3063 (OUTLIER) cc_final: -0.0146 (pmm) REVERT: B 487 MET cc_start: 0.2033 (mpp) cc_final: 0.1550 (mpp) REVERT: B 533 GLU cc_start: 0.2960 (OUTLIER) cc_final: 0.2212 (tp30) outliers start: 36 outliers final: 21 residues processed: 69 average time/residue: 0.4113 time to fit residues: 30.8672 Evaluate side-chains 69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 38 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 209 GLN 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 420 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 533 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 281 HIS B 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.310231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.249946 restraints weight = 26506.214| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 6.66 r_work: 0.4347 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.4347 ------------------------------------------------------------------------------- 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 = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0398 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8987 Z= 0.188 Angle : 0.882 22.991 12219 Z= 0.396 Chirality : 0.048 0.245 1325 Planarity : 0.006 0.061 1590 Dihedral : 7.722 144.164 1274 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 4.73 % Allowed : 25.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1086 helix: 0.56 (0.26), residues: 394 sheet: -0.38 (0.40), residues: 176 loop : -1.01 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 186 TYR 0.020 0.002 TYR B 27 PHE 0.025 0.003 PHE A 168 TRP 0.012 0.001 TRP A 540 HIS 0.007 0.002 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 8980) covalent geometry : angle 0.81780 / 0.40 (12207) hydrogen bonds : bond 0.04125 / 2.81 ( 355) hydrogen bonds : angle 5.24564 / 3.58 ( 1006) metal coordination : bond 0.01099 / 0.54 ( 4) metal coordination : angle 10.57027 / 5.83 ( 12) Misc. bond : bond 0.02336 / 0.87 ( 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 87 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 44 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: -0.0314 (mt-10) cc_final: -0.1765 (tp30) REVERT: A 444 ASN cc_start: 0.0835 (OUTLIER) cc_final: -0.1563 (p0) REVERT: A 486 PHE cc_start: 0.0872 (m-10) cc_final: 0.0536 (m-10) REVERT: A 558 MET cc_start: 0.0573 (OUTLIER) cc_final: -0.0820 (tpp) REVERT: B 121 GLN cc_start: 0.2913 (OUTLIER) cc_final: 0.2594 (mt0) REVERT: B 136 MET cc_start: 0.2962 (pp-130) cc_final: 0.0780 (mmm) REVERT: B 166 LEU cc_start: 0.1455 (OUTLIER) cc_final: 0.0817 (tm) REVERT: B 186 ARG cc_start: -0.0086 (mtt180) cc_final: -0.0744 (tpm170) REVERT: B 209 GLN cc_start: -0.0982 (OUTLIER) cc_final: -0.1895 (pm20) REVERT: B 373 ARG cc_start: -0.1431 (OUTLIER) cc_final: -0.2450 (mtm-85) REVERT: B 375 LEU cc_start: -0.2015 (OUTLIER) cc_final: -0.2256 (mt) REVERT: B 397 ASN cc_start: 0.2960 (m110) cc_final: 0.0793 (t0) REVERT: B 413 LYS cc_start: 0.2771 (OUTLIER) cc_final: 0.2245 (ptpt) REVERT: B 462 MET cc_start: 0.3233 (OUTLIER) cc_final: -0.0007 (pmm) REVERT: B 487 MET cc_start: 0.1983 (mpp) cc_final: 0.1474 (mpp) REVERT: B 557 ILE cc_start: 0.1760 (OUTLIER) cc_final: 0.1286 (tt) outliers start: 43 outliers final: 25 residues processed: 81 average time/residue: 0.3589 time to fit residues: 31.9535 Evaluate side-chains 74 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 39 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 558 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 LYS 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 126 LEU Chi-restraints excluded: chain B residue 128 LYS 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 166 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLN 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 420 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 557 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.0020 chunk 73 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.312732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.269626 restraints weight = 32987.644| |-----------------------------------------------------------------------------| r_work (start): 0.4811 rms_B_bonded: 4.49 r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4815 r_free = 0.4815 target_work(ls_wunit_k1) = 0.267 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4815 r_free = 0.4815 target_work(ls_wunit_k1) = 0.267 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1022 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8987 Z= 0.187 Angle : 0.870 20.467 12219 Z= 0.393 Chirality : 0.047 0.263 1325 Planarity : 0.006 0.062 1590 Dihedral : 7.795 141.496 1274 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 4.29 % Allowed : 26.26 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1086 helix: 0.41 (0.26), residues: 398 sheet: -0.68 (0.37), residues: 196 loop : -1.11 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 186 TYR 0.020 0.002 TYR A 527 PHE 0.024 0.003 PHE A 161 TRP 0.009 0.001 TRP A 197 HIS 0.012 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 8980) covalent geometry : angle 0.81077 / 0.39 (12207) hydrogen bonds : bond 0.03940 / 2.71 ( 355) hydrogen bonds : angle 5.23551 / 3.58 ( 1006) metal coordination : bond 0.01448 / 0.71 ( 4) metal coordination : angle 10.11992 / 5.69 ( 12) Misc. bond : bond 0.03211 / 1.20 ( 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 84 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 45 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.2155 (OUTLIER) cc_final: 0.1905 (pttt) REVERT: A 109 GLU cc_start: -0.0180 (mt-10) cc_final: -0.1242 (tp30) REVERT: A 444 ASN cc_start: 0.1484 (OUTLIER) cc_final: -0.0772 (p0) REVERT: A 532 LEU cc_start: 0.1788 (mp) cc_final: 0.0999 (mt) REVERT: B 121 GLN cc_start: 0.3697 (OUTLIER) cc_final: 0.3450 (mt0) REVERT: B 136 MET cc_start: 0.3839 (OUTLIER) cc_final: 0.1679 (mmm) REVERT: B 166 LEU cc_start: 0.1223 (OUTLIER) cc_final: 0.0512 (tm) REVERT: B 186 ARG cc_start: 0.1419 (mtt180) cc_final: -0.0296 (tpm170) REVERT: B 209 GLN cc_start: 0.1031 (OUTLIER) cc_final: -0.0709 (pm20) REVERT: B 373 ARG cc_start: 0.0398 (OUTLIER) cc_final: -0.1084 (mtm-85) REVERT: B 413 LYS cc_start: 0.2640 (OUTLIER) cc_final: 0.1962 (ptpt) REVERT: B 462 MET cc_start: 0.3239 (OUTLIER) cc_final: 0.0159 (pmm) REVERT: B 487 MET cc_start: 0.1430 (mpp) cc_final: 0.0891 (mpp) outliers start: 39 outliers final: 23 residues processed: 74 average time/residue: 0.4273 time to fit residues: 34.2566 Evaluate side-chains 76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 135 LEU 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 B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 73 LYS 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 128 LYS 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 166 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 HIS ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 233 ASN B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.314300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.259218 restraints weight = 30670.236| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 6.72 r_work: 0.4444 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0450 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8987 Z= 0.198 Angle : 0.894 17.001 12219 Z= 0.411 Chirality : 0.048 0.247 1325 Planarity : 0.007 0.065 1590 Dihedral : 8.016 140.818 1274 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 3.96 % Allowed : 26.92 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1086 helix: 0.23 (0.26), residues: 404 sheet: -0.48 (0.43), residues: 158 loop : -1.17 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 76 TYR 0.021 0.002 TYR A 527 PHE 0.028 0.003 PHE A 168 TRP 0.015 0.001 TRP B 348 HIS 0.011 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 8980) covalent geometry : angle 0.84164 / 0.41 (12207) hydrogen bonds : bond 0.04116 / 2.85 ( 355) hydrogen bonds : angle 5.37558 / 3.68 ( 1006) metal coordination : bond 0.01729 / 0.85 ( 4) metal coordination : angle 9.69482 / 5.52 ( 12) Misc. bond : bond 0.03699 / 1.38 ( 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 76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 40 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: -0.0036 (mt-10) cc_final: -0.1714 (tp30) REVERT: A 444 ASN cc_start: 0.0929 (OUTLIER) cc_final: -0.1227 (p0) REVERT: A 532 LEU cc_start: 0.0924 (mp) cc_final: 0.0519 (mt) REVERT: B 121 GLN cc_start: 0.3176 (OUTLIER) cc_final: 0.2889 (mt0) REVERT: B 136 MET cc_start: 0.3038 (OUTLIER) cc_final: 0.0765 (mmm) REVERT: B 166 LEU cc_start: 0.1400 (OUTLIER) cc_final: 0.0802 (tm) REVERT: B 186 ARG cc_start: 0.0015 (mtt180) cc_final: -0.0663 (tpm170) REVERT: B 209 GLN cc_start: -0.0414 (OUTLIER) cc_final: -0.1415 (pm20) REVERT: B 373 ARG cc_start: -0.1302 (OUTLIER) cc_final: -0.2331 (mtm-85) REVERT: B 413 LYS cc_start: 0.2820 (OUTLIER) cc_final: 0.2278 (ptpt) REVERT: B 462 MET cc_start: 0.3252 (OUTLIER) cc_final: -0.0059 (pmm) REVERT: B 487 MET cc_start: 0.2101 (mpp) cc_final: 0.1504 (mpp) outliers start: 36 outliers final: 21 residues processed: 69 average time/residue: 0.4318 time to fit residues: 32.3580 Evaluate side-chains 68 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 B residue 4 LYS Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 128 LYS 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 166 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 370 TYR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.315231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.258067 restraints weight = 29154.651| |-----------------------------------------------------------------------------| r_work (start): 0.4679 rms_B_bonded: 7.27 r_work: 0.4433 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4441 r_free = 0.4441 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4441 r_free = 0.4441 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0372 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8987 Z= 0.135 Angle : 0.797 17.617 12219 Z= 0.343 Chirality : 0.044 0.169 1325 Planarity : 0.005 0.065 1590 Dihedral : 7.528 140.798 1274 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 2.97 % Allowed : 27.91 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1086 helix: 0.58 (0.27), residues: 405 sheet: -0.81 (0.37), residues: 193 loop : -0.97 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.013 0.001 TYR B 211 PHE 0.014 0.002 PHE A 168 TRP 0.009 0.001 TRP A 542 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8980) covalent geometry : angle 0.72724 / 0.34 (12207) hydrogen bonds : bond 0.03278 / 2.19 ( 355) hydrogen bonds : angle 4.97338 / 3.42 ( 1006) metal coordination : bond 0.00979 / 0.47 ( 4) metal coordination : angle 10.46000 / 5.93 ( 12) Misc. bond : bond 0.01951 / 0.73 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.54 seconds wall clock time: 44 minutes 0.18 seconds (2640.18 seconds total)