Starting phenix.real_space_refine
on Wed Feb  4 14:20:59 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uuo_64513/02_2026/9uuo_64513.cif"
  }
  resolution = 3.68
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      6      6.06       5
     S      58      5.16       5
     C    6998      2.51       5
     N    1880      2.21       5
     O    2062      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11004
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4487
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 21, 'TRANS': 511}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4360
          Classifications: {'peptide': 540}
          Link IDs: {'PTRANS': 23, 'TRANS': 516}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 795
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 804
          Classifications: {'peptide': 100}
          Link IDs: {'TRANS': 99}
    Chain: "E"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 552
          Classifications: {'peptide': 70}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' ZN': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1517  SG  CYS A 303      62.224  46.159  48.960  1.00 58.47           S
  ATOM   1699  SG  CYS A 323      61.038  50.610  48.148  1.00 72.29           S
  ATOM   6229  SG  CYS B 266      23.861  39.559  45.092  1.00 99.86           S
  ATOM   6247  SG  CYS B 269      22.136  36.685  45.756  1.00 96.25           S
  ATOM   6431  SG  CYS B 294      24.160  35.904  48.548  1.00 99.51           S
  ATOM   6643  SG  CYS B 320      35.538  31.969  35.098  1.00 89.31           S
  ATOM   6818  SG  CYS B 343      32.116  29.914  36.061  1.00 84.77           S
  ATOM   7095  SG  CYS B 376      29.116  26.121  26.861  1.00111.31           S
  ATOM   7121  SG  CYS B 379      31.477  28.397  25.711  1.00120.12           S
  ATOM   7304  SG  CYS B 402      29.280  29.705  28.160  1.00 96.65           S
  ATOM   7194  SG  CYS B 389      22.209  19.932  31.540  1.00131.75           S
  ATOM   7239  SG  CYS B 394      22.317  15.723  30.037  1.00145.38           S
  ATOM   6351  SG  CYS B 283      33.583  47.947  41.537  1.00104.32           S
  ATOM   6369  SG  CYS B 286      33.065  45.999  37.997  1.00 99.95           S
  ATOM   6539  SG  CYS B 307      35.686  43.957  41.142  1.00 88.20           S
  ATOM   6567  SG  CYS B 310      36.172  46.879  39.063  1.00 87.00           S

  Time building chain proxies: 2.42, per 1000 atoms: 0.22
  Number of scatterers: 11004
  At special positions: 0
  Unit cell: (96.512, 94.016, 117.312, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      6     29.99
     S      58     16.00
     O    2062      8.00
     N    1880      7.00
     C    6998      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=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 390.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 323 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 303 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 319 "
      pdb="  ZN B 801 "
        pdb="ZN    ZN B 801 " - pdb=" ND1 HIS B 291 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS B 269 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS B 266 "
        pdb="ZN    ZN B 801 " - pdb=" SG  CYS B 294 "
      pdb="  ZN B 802 "
        pdb="ZN    ZN B 802 " - pdb=" ND1 HIS B 340 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 343 "
        pdb="ZN    ZN B 802 " - pdb=" SG  CYS B 320 "
      pdb="  ZN B 803 "
        pdb="ZN    ZN B 803 " - pdb=" SG  CYS B 376 "
        pdb="ZN    ZN B 803 " - pdb=" SG  CYS B 402 "
        pdb="ZN    ZN B 803 " - pdb=" SG  CYS B 379 "
      pdb="  ZN B 804 "
        pdb="ZN    ZN B 804 " - pdb=" ND1 HIS B 438 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 389 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 394 "
      pdb="  ZN B 805 "
        pdb="ZN    ZN B 805 " - pdb=" SG  CYS B 310 "
        pdb="ZN    ZN B 805 " - pdb=" SG  CYS B 286 "
        pdb="ZN    ZN B 805 " - pdb=" SG  CYS B 307 "
        pdb="ZN    ZN B 805 " - pdb=" SG  CYS B 283 "
      Number of angles added : 9


  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2570

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 11 sheets defined
      48.3% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 127 through 139
    Processing helix  chain 'A' and resid 140 through 142
      No H-bonds generated for 'chain 'A' and resid 140 through 142'
    Processing helix  chain 'A' and resid 153 through 166
    Processing helix  chain 'A' and resid 189 through 193
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 202 through 207
    Processing helix  chain 'A' and resid 214 through 233
      removed outlier: 4.218A  pdb=" N   SER A 230 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   ALA A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 312 through 323
    Processing helix  chain 'A' and resid 349 through 361
      removed outlier: 3.760A  pdb=" N   CYS A 353 " --> pdb=" O   ASN A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 426
    Processing helix  chain 'A' and resid 429 through 446
    Processing helix  chain 'A' and resid 456 through 485
    Processing helix  chain 'A' and resid 498 through 507
      removed outlier: 3.800A  pdb=" N   LEU A 505 " --> pdb=" O   ASP A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 518
    Processing helix  chain 'A' and resid 545 through 558
      removed outlier: 4.884A  pdb=" N   TRP A 556 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER A 557 " --> pdb=" O   TYR A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 625
      removed outlier: 3.907A  pdb=" N   HIS A 622 " --> pdb=" O   ASN A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 669
      removed outlier: 3.639A  pdb=" N   ASP A 669 " --> pdb=" O   TYR A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 693
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 161 through 175
      removed outlier: 4.000A  pdb=" N   SER B 175 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 179
      removed outlier: 3.681A  pdb=" N   VAL B 179 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 176 through 179'
    Processing helix  chain 'B' and resid 188 through 202
      removed outlier: 3.617A  pdb=" N   LEU B 193 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 229
    Processing helix  chain 'B' and resid 234 through 252
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 307 through 313
    Processing helix  chain 'B' and resid 341 through 347
    Processing helix  chain 'B' and resid 368 through 374
      removed outlier: 3.756A  pdb=" N   TRP B 372 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 406
    Processing helix  chain 'B' and resid 416 through 421
    Processing helix  chain 'B' and resid 446 through 466
    Processing helix  chain 'B' and resid 496 through 511
    Processing helix  chain 'B' and resid 515 through 534
    Processing helix  chain 'B' and resid 551 through 602
      removed outlier: 4.824A  pdb=" N   ILE B 599 " --> pdb=" O   LYS B 595 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 17
      removed outlier: 4.158A  pdb=" N   SER C  16 " --> pdb=" O   ASP C  12 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE C  17 " --> pdb=" O   ILE C  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 12 through 17'
    Processing helix  chain 'C' and resid 17 through 41
      removed outlier: 4.175A  pdb=" N   LEU C  24 " --> pdb=" O   THR C  20 " (cutoff:3.500A)
      Proline residue:  C  25  - end of helix
    Processing helix  chain 'C' and resid 46 through 97
    Processing helix  chain 'C' and resid 98 through 102
      removed outlier: 3.899A  pdb=" N   SER C 101 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 52
      removed outlier: 4.157A  pdb=" N   ASN F  47 " --> pdb=" O   TYR F  43 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   SER F  48 " --> pdb=" O   PHE F  44 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   HIS F  52 " --> pdb=" O   SER F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 98
    Processing helix  chain 'F' and resid 99 through 110
      removed outlier: 3.691A  pdb=" N   VAL F 103 " --> pdb=" O   SER F  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 189
    Processing helix  chain 'E' and resid 190 through 204
    Processing helix  chain 'E' and resid 228 through 244
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.862A  pdb=" N   LYS A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE E 222 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276
    Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 302
    Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 336
      removed outlier: 6.300A  pdb=" N   GLU A 332 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   GLU A 343 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   TYR A 334 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR A 379 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   GLU A 383 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   PHE A 400 " --> pdb=" O   GLU A 383 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   GLU A 385 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   PHE A 398 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494
    Processing sheet with id=AA6, first strand: chain 'A' and resid 496 through 497
      removed outlier: 7.569A  pdb=" N   TYR A 539 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ILE B  34 " --> pdb=" O   TYR A 539 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   ILE A 541 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 584 through 586
    Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 282
      removed outlier: 3.632A  pdb=" N   VAL B 290 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 339 through 340
      removed outlier: 9.020A  pdb=" N   ILE B 361 " --> pdb=" O   PHE B 330 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   GLN B 332 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 387 through 388
    Processing sheet with id=AB2, first strand: chain 'B' and resid 410 through 411

    492 hydrogen bonds defined for protein.
    1416 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: 1.42

  Time building geometry restraints manager: 1.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 3540
        1.34 -     1.46: 2715
        1.46 -     1.58: 4915
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 11251
  Sorted by residual:
  bond pdb=" CA  PRO A 289 "
       pdb=" C   PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.528  1.514  0.014 9.10e-03 1.21e+04 2.34e+00
  bond pdb=" C   LEU B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.333  1.320  0.013 1.01e-02 9.80e+03 1.78e+00
  bond pdb=" C   CYS B 323 "
       pdb=" N   PRO B 324 "
    ideal  model  delta    sigma   weight residual
    1.336  1.320  0.016 1.20e-02 6.94e+03 1.77e+00
  bond pdb=" C   ALA B 155 "
       pdb=" N   PRO B 156 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.45e+00
  bond pdb=" N   ILE B  72 "
       pdb=" CA  ILE B  72 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.019 1.57e-02 4.06e+03 1.44e+00
  ... (remaining 11246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 14958
        2.06 -     4.13: 199
        4.13 -     6.19: 23
        6.19 -     8.25: 2
        8.25 -    10.32: 1
  Bond angle restraints: 15183
  Sorted by residual:
  angle pdb=" N   VAL A 267 "
        pdb=" CA  VAL A 267 "
        pdb=" C   VAL A 267 "
      ideal   model   delta    sigma   weight residual
     113.71  108.51    5.20 9.50e-01 1.11e+00 3.00e+01
  angle pdb=" N   VAL A 522 "
        pdb=" CA  VAL A 522 "
        pdb=" C   VAL A 522 "
      ideal   model   delta    sigma   weight residual
     113.20  109.21    3.99 9.60e-01 1.09e+00 1.72e+01
  angle pdb=" CA  LEU A 663 "
        pdb=" CB  LEU A 663 "
        pdb=" CG  LEU A 663 "
      ideal   model   delta    sigma   weight residual
     116.30  126.62  -10.32 3.50e+00 8.16e-02 8.69e+00
  angle pdb=" C   LYS B 228 "
        pdb=" N   HIS B 229 "
        pdb=" CA  HIS B 229 "
      ideal   model   delta    sigma   weight residual
     122.31  116.63    5.68 2.00e+00 2.50e-01 8.07e+00
  angle pdb=" C   SER B 422 "
        pdb=" N   ASN B 423 "
        pdb=" CA  ASN B 423 "
      ideal   model   delta    sigma   weight residual
     121.54  126.60   -5.06 1.91e+00 2.74e-01 7.02e+00
  ... (remaining 15178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 6003
       17.96 -    35.92: 643
       35.92 -    53.88: 105
       53.88 -    71.84: 15
       71.84 -    89.79: 14
  Dihedral angle restraints: 6780
    sinusoidal: 2819
      harmonic: 3961
  Sorted by residual:
  dihedral pdb=" CA  ALA B 155 "
           pdb=" C   ALA B 155 "
           pdb=" N   PRO B 156 "
           pdb=" CA  PRO B 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.79  -43.21     0      5.00e+00 4.00e-02 7.47e+01
  dihedral pdb=" CA  LEU A 277 "
           pdb=" C   LEU A 277 "
           pdb=" N   ARG A 278 "
           pdb=" CA  ARG A 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.67  -25.33     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  SER B 313 "
           pdb=" C   SER B 313 "
           pdb=" N   LYS B 314 "
           pdb=" CA  LYS B 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.15  -24.85     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 6777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 977
       0.031 -    0.063: 455
       0.063 -    0.094: 138
       0.094 -    0.126: 56
       0.126 -    0.157: 8
  Chirality restraints: 1634
  Sorted by residual:
  chirality pdb=" CG  LEU A 277 "
            pdb=" CB  LEU A 277 "
            pdb=" CD1 LEU A 277 "
            pdb=" CD2 LEU A 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.18e-01
  chirality pdb=" CA  PRO B 156 "
            pdb=" N   PRO B 156 "
            pdb=" C   PRO B 156 "
            pdb=" CB  PRO B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CB  ILE B 158 "
            pdb=" CA  ILE B 158 "
            pdb=" CG1 ILE B 158 "
            pdb=" CG2 ILE B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 1631 not shown)

  Planarity restraints: 1941
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 155 "   -0.055 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO B 156 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 156 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 156 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 577 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.22e+00
        pdb=" N   PRO A 578 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 578 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 578 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 514 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO B 515 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 515 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 515 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1938 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 237
        2.65 -     3.21: 11281
        3.21 -     3.77: 17608
        3.77 -     4.34: 23389
        4.34 -     4.90: 37190
  Nonbonded interactions: 89705
  Sorted by model distance:
  nonbonded pdb=" N   CYS B 379 "
            pdb="ZN    ZN B 803 "
     model   vdw
     2.087 2.310
  nonbonded pdb=" ND2 ASN A 295 "
            pdb=" O   THR B 335 "
     model   vdw
     2.109 3.120
  nonbonded pdb=" OD1 ASP B 191 "
            pdb=" OH  TYR B 525 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OH  TYR B 185 "
            pdb=" OD2 ASP B 191 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" O   GLN B 184 "
            pdb=" OG1 THR B 539 "
     model   vdw
     2.150 3.040
  ... (remaining 89700 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.280
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.011   0.682  11271  Z= 0.408
  Angle     :  0.934  64.636  15192  Z= 0.401
  Chirality :  0.042   0.157   1634
  Planarity :  0.004   0.083   1941
  Dihedral  : 15.085  89.795   4210
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -3.32 (0.19), residues: 1318
  helix: -1.28 (0.18), residues: 575
  sheet: -3.66 (0.47), residues: 70
  loop : -2.94 (0.21), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  93 
 TYR   0.018   0.001   TYR A 463 
 PHE   0.026   0.002   PHE B 561 
 TRP   0.022   0.002   TRP B 223 
 HIS   0.005   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (11251)
  covalent geometry    : angle       0.64003 (15183)
  hydrogen bonds       : bond        0.10874 (  492)
  hydrogen bonds       : angle       5.71911 ( 1416)
  metal coordination   : bond        0.24467 (   20)
  metal coordination   : angle      27.95473 (    9)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 MET cc_start: 0.3400 (mmm) cc_final: 0.3104 (mtp)
REVERT: A  193 TYR cc_start: 0.8482 (m-80) cc_final: 0.8254 (m-10)
REVERT: A  203 MET cc_start: 0.7941 (tpp) cc_final: 0.7524 (tpp)
REVERT: A  334 TYR cc_start: 0.8118 (t80) cc_final: 0.7541 (t80)
REVERT: A  473 GLU cc_start: 0.8461 (tt0) cc_final: 0.8117 (tt0)
REVERT: B  119 ARG cc_start: 0.7008 (mmp-170) cc_final: 0.6670 (mmp-170)
REVERT: B  182 LYS cc_start: 0.8303 (tptm) cc_final: 0.8041 (tptm)
REVERT: B  224 PHE cc_start: 0.7255 (t80) cc_final: 0.7014 (t80)
REVERT: B  528 MET cc_start: 0.8479 (mtm) cc_final: 0.8182 (mtm)
REVERT: B  543 GLU cc_start: 0.7070 (mp0) cc_final: 0.6739 (mp0)
REVERT: B  569 LEU cc_start: 0.9433 (mp) cc_final: 0.9207 (mp)
REVERT: C   13 ILE cc_start: 0.8990 (tt) cc_final: 0.8779 (tt)
REVERT: C   23 HIS cc_start: 0.7416 (m-70) cc_final: 0.7106 (m90)
REVERT: C   52 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8716 (ptp-110)
REVERT: C   70 ASP cc_start: 0.8049 (t70) cc_final: 0.7815 (t0)
REVERT: F   34 GLN cc_start: 0.8372 (tp40) cc_final: 0.7948 (tp-100)
REVERT: F   35 GLU cc_start: 0.8832 (tp30) cc_final: 0.8393 (tp30)
REVERT: F   39 LYS cc_start: 0.9055 (tptt) cc_final: 0.8814 (tppt)
REVERT: F   71 LYS cc_start: 0.8795 (tppt) cc_final: 0.8154 (tptp)
REVERT: F  102 TYR cc_start: 0.8919 (t80) cc_final: 0.8620 (t80)
REVERT: E  214 ASN cc_start: 0.9168 (t0) cc_final: 0.8926 (t0)
REVERT: E  220 PHE cc_start: 0.7574 (t80) cc_final: 0.6799 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1086
  time to fit residues: 42.4757
Evaluate side-chains
  217 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 ASN
A 583 ASN
A 691 HIS
B 122 HIS
B 169 GLN
B 177 ASN
B 190 GLN
B 276 ASN
B 315 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 388 GLN
B 464 GLN
B 497 HIS
B 504 GLN
B 565 GLN
C  23 HIS
C  71 GLN
C  78 HIS
F  49 ASN
F  52 HIS
F  64 HIS
F  68 ASN
F  83 HIS
F 105 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.142637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.110175 restraints weight = 21776.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.113680 restraints weight = 12046.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.115906 restraints weight = 8526.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.117376 restraints weight = 6964.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118274 restraints weight = 6148.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11271  Z= 0.162
  Angle     :  0.629  13.567  15192  Z= 0.317
  Chirality :  0.042   0.175   1634
  Planarity :  0.004   0.086   1941
  Dihedral  :  5.273  42.406   1455
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.17 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -1.89 (0.21), residues: 1318
  helix: -0.03 (0.20), residues: 612
  sheet: -2.98 (0.54), residues: 70
  loop : -2.33 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  93 
 TYR   0.022   0.002   TYR F  37 
 PHE   0.023   0.002   PHE A 206 
 TRP   0.027   0.002   TRP A 268 
 HIS   0.005   0.001   HIS B 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (11251)
  covalent geometry    : angle       0.61171 (15183)
  hydrogen bonds       : bond        0.04476 (  492)
  hydrogen bonds       : angle       4.81975 ( 1416)
  metal coordination   : bond        0.01609 (   20)
  metal coordination   : angle       6.00776 (    9)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 259
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 ARG cc_start: 0.6555 (ttt90) cc_final: 0.6327 (mtm-85)
REVERT: A  173 MET cc_start: 0.3467 (mmm) cc_final: 0.3249 (mmp)
REVERT: A  203 MET cc_start: 0.7861 (tpp) cc_final: 0.7483 (tpp)
REVERT: A  273 GLU cc_start: 0.7910 (tt0) cc_final: 0.7570 (tm-30)
REVERT: A  309 TYR cc_start: 0.8815 (p90) cc_final: 0.8560 (p90)
REVERT: A  334 TYR cc_start: 0.8193 (t80) cc_final: 0.7628 (t80)
REVERT: A  382 THR cc_start: 0.9193 (t) cc_final: 0.8960 (p)
REVERT: A  518 GLU cc_start: 0.7862 (pt0) cc_final: 0.7043 (tp30)
REVERT: A  553 TYR cc_start: 0.8557 (t80) cc_final: 0.8280 (t80)
REVERT: A  583 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8730 (t0)
REVERT: B  119 ARG cc_start: 0.6921 (mmp-170) cc_final: 0.6719 (mmp-170)
REVERT: B  224 PHE cc_start: 0.7464 (t80) cc_final: 0.7056 (t80)
REVERT: B  256 ASP cc_start: 0.8908 (m-30) cc_final: 0.8570 (m-30)
REVERT: B  316 ASN cc_start: 0.7116 (t0) cc_final: 0.6857 (t0)
REVERT: B  521 ASP cc_start: 0.8285 (t0) cc_final: 0.7795 (t0)
REVERT: B  528 MET cc_start: 0.8650 (mtm) cc_final: 0.8339 (mtm)
REVERT: B  543 GLU cc_start: 0.7028 (mp0) cc_final: 0.6687 (mp0)
REVERT: C   70 ASP cc_start: 0.8171 (t70) cc_final: 0.7881 (t0)
REVERT: F   35 GLU cc_start: 0.8898 (tp30) cc_final: 0.8458 (tp30)
REVERT: F   39 LYS cc_start: 0.9043 (tptt) cc_final: 0.8808 (tppt)
REVERT: F   40 GLU cc_start: 0.8355 (tt0) cc_final: 0.7983 (tt0)
REVERT: F   65 TYR cc_start: 0.5551 (OUTLIER) cc_final: 0.2342 (p90)
REVERT: F  102 TYR cc_start: 0.8958 (t80) cc_final: 0.8631 (t80)
  outliers start: 31
  outliers final: 18
  residues processed: 272
  average time/residue: 0.0972
  time to fit residues: 38.2273
Evaluate side-chains
  247 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 227
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  583 ASN
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  184 PHE
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 79 optimal weight:    9.9990
   chunk 84 optimal weight:    0.0020
   chunk 61 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0370
   chunk 98 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.2866

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 ASN
F  52 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.148991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.117887 restraints weight = 21866.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.121483 restraints weight = 11794.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.123837 restraints weight = 8174.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.125053 restraints weight = 6572.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.126127 restraints weight = 5846.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11271  Z= 0.121
  Angle     :  0.578  13.749  15192  Z= 0.293
  Chirality :  0.041   0.169   1634
  Planarity :  0.004   0.078   1941
  Dihedral  :  4.888  39.224   1455
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.76 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -1.05 (0.23), residues: 1318
  helix:  0.57 (0.20), residues: 616
  sheet: -2.55 (0.56), residues: 70
  loop : -1.79 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  93 
 TYR   0.020   0.001   TYR B 295 
 PHE   0.023   0.002   PHE A 206 
 TRP   0.027   0.002   TRP A 268 
 HIS   0.008   0.001   HIS C  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (11251)
  covalent geometry    : angle       0.57044 (15183)
  hydrogen bonds       : bond        0.04024 (  492)
  hydrogen bonds       : angle       4.51498 ( 1416)
  metal coordination   : bond        0.00903 (   20)
  metal coordination   : angle       3.77575 (    9)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 258
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.7766 (tpp) cc_final: 0.7369 (tpp)
REVERT: A  334 TYR cc_start: 0.8088 (t80) cc_final: 0.7743 (t80)
REVERT: B  165 LYS cc_start: 0.9232 (tppt) cc_final: 0.8703 (tppt)
REVERT: B  224 PHE cc_start: 0.7311 (t80) cc_final: 0.6985 (t80)
REVERT: B  227 GLU cc_start: 0.8687 (tp30) cc_final: 0.8321 (tp30)
REVERT: B  316 ASN cc_start: 0.6826 (t0) cc_final: 0.6594 (t0)
REVERT: B  358 MET cc_start: 0.7223 (mmm) cc_final: 0.6946 (mmm)
REVERT: B  487 LYS cc_start: 0.8404 (mttt) cc_final: 0.8100 (mttt)
REVERT: B  521 ASP cc_start: 0.8183 (t0) cc_final: 0.7808 (t0)
REVERT: B  528 MET cc_start: 0.8551 (mtm) cc_final: 0.8333 (mtm)
REVERT: C   50 MET cc_start: 0.8789 (ppp) cc_final: 0.8529 (ptp)
REVERT: F   22 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7541 (mtm180)
REVERT: F   34 GLN cc_start: 0.8719 (pt0) cc_final: 0.8337 (tp-100)
REVERT: F   35 GLU cc_start: 0.8775 (tp30) cc_final: 0.8404 (tp30)
REVERT: F   38 ASP cc_start: 0.8582 (p0) cc_final: 0.8247 (p0)
REVERT: F   65 TYR cc_start: 0.5465 (OUTLIER) cc_final: 0.2160 (p90)
REVERT: F  102 TYR cc_start: 0.8843 (t80) cc_final: 0.8500 (t80)
REVERT: E  192 ASP cc_start: 0.7951 (m-30) cc_final: 0.7675 (m-30)
  outliers start: 35
  outliers final: 17
  residues processed: 276
  average time/residue: 0.0942
  time to fit residues: 37.6296
Evaluate side-chains
  246 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain E residue  184 PHE
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 583 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 451 ASN
C  73 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.144817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.112986 restraints weight = 22021.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.116431 restraints weight = 12445.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.118620 restraints weight = 8900.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.120042 restraints weight = 7298.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.120453 restraints weight = 6466.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  11271  Z= 0.173
  Angle     :  0.625  14.545  15192  Z= 0.314
  Chirality :  0.042   0.190   1634
  Planarity :  0.004   0.075   1941
  Dihedral  :  4.902  39.294   1455
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.29 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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 (0.23), residues: 1318
  helix:  0.69 (0.21), residues: 617
  sheet: -2.46 (0.56), residues: 70
  loop : -1.62 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 157 
 TYR   0.018   0.001   TYR B 295 
 PHE   0.024   0.002   PHE B 509 
 TRP   0.046   0.002   TRP A 268 
 HIS   0.009   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (11251)
  covalent geometry    : angle       0.61703 (15183)
  hydrogen bonds       : bond        0.04243 (  492)
  hydrogen bonds       : angle       4.60568 ( 1416)
  metal coordination   : bond        0.01354 (   20)
  metal coordination   : angle       4.11171 (    9)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 230
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.7822 (tpp) cc_final: 0.7482 (tpp)
REVERT: A  273 GLU cc_start: 0.7902 (tt0) cc_final: 0.7668 (tm-30)
REVERT: A  334 TYR cc_start: 0.8270 (t80) cc_final: 0.7743 (t80)
REVERT: A  518 GLU cc_start: 0.7768 (pt0) cc_final: 0.6900 (tp30)
REVERT: B  165 LYS cc_start: 0.9263 (tppt) cc_final: 0.8714 (tppt)
REVERT: B  224 PHE cc_start: 0.7502 (t80) cc_final: 0.7284 (t80)
REVERT: B  227 GLU cc_start: 0.8750 (tp30) cc_final: 0.8382 (tp30)
REVERT: B  316 ASN cc_start: 0.7117 (t0) cc_final: 0.6811 (t0)
REVERT: B  494 VAL cc_start: 0.8353 (t) cc_final: 0.8077 (t)
REVERT: B  521 ASP cc_start: 0.8189 (t0) cc_final: 0.7817 (t0)
REVERT: C   50 MET cc_start: 0.8844 (ppp) cc_final: 0.8461 (ppp)
REVERT: F   22 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7593 (mtm180)
REVERT: F   35 GLU cc_start: 0.8774 (tp30) cc_final: 0.8485 (tp30)
REVERT: F   65 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.2121 (p90)
REVERT: F  102 TYR cc_start: 0.8911 (t80) cc_final: 0.8596 (t80)
  outliers start: 43
  outliers final: 31
  residues processed: 253
  average time/residue: 0.0896
  time to fit residues: 32.9023
Evaluate side-chains
  247 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 215
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain E residue  184 PHE
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0980
   chunk 2 optimal weight:    6.9990
   chunk 120 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 ASN
** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.146505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.114783 restraints weight = 21919.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.118315 restraints weight = 12362.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.120594 restraints weight = 8777.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.122016 restraints weight = 7167.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.122717 restraints weight = 6347.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11271  Z= 0.138
  Angle     :  0.615  14.543  15192  Z= 0.308
  Chirality :  0.042   0.178   1634
  Planarity :  0.004   0.071   1941
  Dihedral  :  4.815  37.730   1455
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.45 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -0.61 (0.23), residues: 1318
  helix:  0.82 (0.21), residues: 617
  sheet: -2.23 (0.58), residues: 70
  loop : -1.45 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 157 
 TYR   0.018   0.001   TYR A 566 
 PHE   0.027   0.002   PHE F  29 
 TRP   0.051   0.002   TRP A 268 
 HIS   0.015   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11251)
  covalent geometry    : angle       0.61036 (15183)
  hydrogen bonds       : bond        0.04099 (  492)
  hydrogen bonds       : angle       4.53404 ( 1416)
  metal coordination   : bond        0.01134 (   20)
  metal coordination   : angle       3.18972 (    9)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 237
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.7796 (tpp) cc_final: 0.7459 (tpp)
REVERT: A  334 TYR cc_start: 0.8222 (t80) cc_final: 0.7677 (t80)
REVERT: A  477 LYS cc_start: 0.8697 (mttt) cc_final: 0.8470 (mtpp)
REVERT: A  518 GLU cc_start: 0.7778 (pt0) cc_final: 0.6894 (tp30)
REVERT: A  576 LEU cc_start: 0.8669 (mt) cc_final: 0.8396 (mp)
REVERT: A  625 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6293 (tpt-90)
REVERT: B  227 GLU cc_start: 0.8740 (tp30) cc_final: 0.8353 (tp30)
REVERT: B  316 ASN cc_start: 0.6991 (t0) cc_final: 0.6751 (t0)
REVERT: B  494 VAL cc_start: 0.8226 (t) cc_final: 0.7914 (t)
REVERT: B  521 ASP cc_start: 0.8207 (t0) cc_final: 0.7897 (t0)
REVERT: B  575 LEU cc_start: 0.8898 (mt) cc_final: 0.8669 (mt)
REVERT: C   50 MET cc_start: 0.8811 (ppp) cc_final: 0.8421 (ppp)
REVERT: C   51 GLU cc_start: 0.8794 (tp30) cc_final: 0.8366 (tm-30)
REVERT: F   22 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.7601 (mtm180)
REVERT: F   34 GLN cc_start: 0.8655 (pt0) cc_final: 0.8283 (tp-100)
REVERT: F   35 GLU cc_start: 0.8810 (tp30) cc_final: 0.8403 (tp30)
REVERT: F   38 ASP cc_start: 0.8725 (p0) cc_final: 0.8504 (p0)
REVERT: F   65 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.2070 (p90)
REVERT: F   95 PHE cc_start: 0.8738 (m-80) cc_final: 0.8378 (m-10)
REVERT: F  102 TYR cc_start: 0.8874 (t80) cc_final: 0.8564 (t80)
REVERT: E  178 ASP cc_start: 0.8273 (p0) cc_final: 0.7871 (p0)
REVERT: E  233 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7583 (tmtt)
  outliers start: 43
  outliers final: 34
  residues processed: 262
  average time/residue: 0.0861
  time to fit residues: 32.8173
Evaluate side-chains
  251 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 216
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  549 ILE
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9990
   chunk 131 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 54 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 ASN
B 209 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.147904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.116315 restraints weight = 21963.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119912 restraints weight = 12314.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.122257 restraints weight = 8714.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123699 restraints weight = 7062.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.124597 restraints weight = 6231.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11271  Z= 0.127
  Angle     :  0.612  14.210  15192  Z= 0.306
  Chirality :  0.042   0.190   1634
  Planarity :  0.004   0.064   1941
  Dihedral  :  4.714  35.295   1455
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.26 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -0.50 (0.23), residues: 1318
  helix:  0.82 (0.21), residues: 616
  sheet: -2.10 (0.59), residues: 70
  loop : -1.28 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 157 
 TYR   0.019   0.001   TYR B 295 
 PHE   0.023   0.001   PHE A 206 
 TRP   0.047   0.002   TRP A 268 
 HIS   0.006   0.001   HIS C  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (11251)
  covalent geometry    : angle       0.60952 (15183)
  hydrogen bonds       : bond        0.04058 (  492)
  hydrogen bonds       : angle       4.53827 ( 1416)
  metal coordination   : bond        0.00961 (   20)
  metal coordination   : angle       2.55077 (    9)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 233
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 MET cc_start: 0.4822 (mmp) cc_final: 0.4419 (mmm)
REVERT: A  203 MET cc_start: 0.7771 (tpp) cc_final: 0.7410 (tpp)
REVERT: A  268 TRP cc_start: 0.7008 (m-10) cc_final: 0.6432 (m-10)
REVERT: A  334 TYR cc_start: 0.8190 (t80) cc_final: 0.7616 (t80)
REVERT: A  477 LYS cc_start: 0.8672 (mttt) cc_final: 0.8407 (mtpp)
REVERT: A  540 ILE cc_start: 0.8324 (pt) cc_final: 0.7804 (mt)
REVERT: A  576 LEU cc_start: 0.8552 (mt) cc_final: 0.8298 (mp)
REVERT: A  583 ASN cc_start: 0.9362 (OUTLIER) cc_final: 0.9053 (t0)
REVERT: A  625 ARG cc_start: 0.6595 (ttp80) cc_final: 0.6312 (tpt-90)
REVERT: B  227 GLU cc_start: 0.8751 (tp30) cc_final: 0.8400 (tp30)
REVERT: B  316 ASN cc_start: 0.6992 (t0) cc_final: 0.6775 (t0)
REVERT: B  341 ASN cc_start: 0.7705 (m-40) cc_final: 0.7378 (m-40)
REVERT: B  494 VAL cc_start: 0.8178 (t) cc_final: 0.7882 (t)
REVERT: B  575 LEU cc_start: 0.8880 (mt) cc_final: 0.8566 (mt)
REVERT: C   50 MET cc_start: 0.8820 (ppp) cc_final: 0.8435 (ppp)
REVERT: C   51 GLU cc_start: 0.8777 (tp30) cc_final: 0.8337 (tm-30)
REVERT: F   22 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7634 (mtp180)
REVERT: F   31 ASN cc_start: 0.8666 (p0) cc_final: 0.8378 (p0)
REVERT: F   34 GLN cc_start: 0.8665 (pt0) cc_final: 0.8248 (tp-100)
REVERT: F   35 GLU cc_start: 0.8770 (tp30) cc_final: 0.8350 (tp30)
REVERT: F   38 ASP cc_start: 0.8653 (p0) cc_final: 0.8432 (p0)
REVERT: F   65 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.2003 (p90)
REVERT: F   97 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8214 (mt)
REVERT: F  102 TYR cc_start: 0.8821 (t80) cc_final: 0.8505 (t80)
REVERT: E  180 GLU cc_start: 0.6059 (pm20) cc_final: 0.5833 (pp20)
REVERT: E  219 GLU cc_start: 0.7706 (pm20) cc_final: 0.7318 (pm20)
REVERT: E  220 PHE cc_start: 0.7001 (t80) cc_final: 0.6710 (t80)
REVERT: E  222 ILE cc_start: 0.8845 (mp) cc_final: 0.8560 (mp)
  outliers start: 44
  outliers final: 32
  residues processed: 257
  average time/residue: 0.0918
  time to fit residues: 34.0935
Evaluate side-chains
  252 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  583 ASN
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   41 THR
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   94 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0010
   chunk 91 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 ASN
B 184 GLN
C  73 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.147557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.116082 restraints weight = 21798.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.119621 restraints weight = 12328.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.121868 restraints weight = 8769.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.123318 restraints weight = 7159.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.124241 restraints weight = 6319.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11271  Z= 0.142
  Angle     :  0.641  14.713  15192  Z= 0.317
  Chirality :  0.043   0.199   1634
  Planarity :  0.004   0.058   1941
  Dihedral  :  4.688  32.920   1455
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.66 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    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: -0.48 (0.23), residues: 1318
  helix:  0.82 (0.21), residues: 616
  sheet: -2.06 (0.58), residues: 70
  loop : -1.26 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 157 
 TYR   0.019   0.001   TYR B 456 
 PHE   0.029   0.002   PHE F  29 
 TRP   0.041   0.002   TRP A 268 
 HIS   0.011   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11251)
  covalent geometry    : angle       0.63696 (15183)
  hydrogen bonds       : bond        0.04085 (  492)
  hydrogen bonds       : angle       4.60061 ( 1416)
  metal coordination   : bond        0.01101 (   20)
  metal coordination   : angle       2.87992 (    9)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 231
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 MET cc_start: 0.4752 (mmp) cc_final: 0.4306 (mmm)
REVERT: A  203 MET cc_start: 0.7821 (tpp) cc_final: 0.7461 (tpp)
REVERT: A  334 TYR cc_start: 0.8244 (t80) cc_final: 0.7695 (t80)
REVERT: A  576 LEU cc_start: 0.8534 (mt) cc_final: 0.8305 (mp)
REVERT: A  583 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9095 (t0)
REVERT: A  625 ARG cc_start: 0.6586 (ttp80) cc_final: 0.6335 (tpt-90)
REVERT: B  165 LYS cc_start: 0.9091 (tppt) cc_final: 0.8655 (tppt)
REVERT: B  227 GLU cc_start: 0.8737 (tp30) cc_final: 0.8418 (tp30)
REVERT: B  316 ASN cc_start: 0.7054 (t0) cc_final: 0.6834 (t0)
REVERT: B  494 VAL cc_start: 0.8162 (t) cc_final: 0.7855 (t)
REVERT: B  528 MET cc_start: 0.8622 (mtm) cc_final: 0.8402 (mtm)
REVERT: C   50 MET cc_start: 0.8798 (ppp) cc_final: 0.8417 (ppp)
REVERT: C   51 GLU cc_start: 0.8765 (tp30) cc_final: 0.8314 (tm-30)
REVERT: F   22 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7591 (mtp180)
REVERT: F   34 GLN cc_start: 0.8663 (pt0) cc_final: 0.8162 (tp-100)
REVERT: F   35 GLU cc_start: 0.8767 (tp30) cc_final: 0.8344 (tp30)
REVERT: F   38 ASP cc_start: 0.8630 (p0) cc_final: 0.8401 (p0)
REVERT: F   65 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.2030 (p90)
REVERT: F   97 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8221 (mt)
REVERT: F  102 TYR cc_start: 0.8804 (t80) cc_final: 0.8477 (t80)
REVERT: E  219 GLU cc_start: 0.7616 (pm20) cc_final: 0.7374 (pm20)
  outliers start: 47
  outliers final: 39
  residues processed: 260
  average time/residue: 0.0945
  time to fit residues: 35.7022
Evaluate side-chains
  264 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  583 ASN
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   41 THR
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   94 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  211 VAL
Chi-restraints excluded: chain E residue  215 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 67 optimal weight:    0.0970
   chunk 75 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 90 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   chunk 84 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 583 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.149578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.118287 restraints weight = 21749.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.121963 restraints weight = 12209.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.124292 restraints weight = 8616.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.125472 restraints weight = 6986.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.125473 restraints weight = 6226.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11271  Z= 0.125
  Angle     :  0.637  14.781  15192  Z= 0.316
  Chirality :  0.042   0.207   1634
  Planarity :  0.004   0.046   1941
  Dihedral  :  4.574  26.459   1455
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.71 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.23), residues: 1318
  helix:  0.86 (0.21), residues: 617
  sheet: -1.98 (0.58), residues: 70
  loop : -1.19 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 157 
 TYR   0.023   0.001   TYR B 295 
 PHE   0.034   0.002   PHE F  29 
 TRP   0.031   0.002   TRP A 268 
 HIS   0.018   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11251)
  covalent geometry    : angle       0.63424 (15183)
  hydrogen bonds       : bond        0.03922 (  492)
  hydrogen bonds       : angle       4.60628 ( 1416)
  metal coordination   : bond        0.00811 (   20)
  metal coordination   : angle       2.41692 (    9)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 238
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8776 (tppp) cc_final: 0.8556 (mmtt)
REVERT: A  203 MET cc_start: 0.7784 (tpp) cc_final: 0.7427 (tpp)
REVERT: A  334 TYR cc_start: 0.8205 (t80) cc_final: 0.7625 (t80)
REVERT: A  540 ILE cc_start: 0.8352 (pt) cc_final: 0.7839 (mt)
REVERT: A  576 LEU cc_start: 0.8473 (mt) cc_final: 0.8211 (mp)
REVERT: A  625 ARG cc_start: 0.6615 (ttp80) cc_final: 0.6362 (tpt-90)
REVERT: B   22 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8193 (p90)
REVERT: B  165 LYS cc_start: 0.9105 (tppt) cc_final: 0.8673 (tppt)
REVERT: B  207 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6177 (ttp)
REVERT: B  227 GLU cc_start: 0.8692 (tp30) cc_final: 0.8426 (tt0)
REVERT: B  316 ASN cc_start: 0.6890 (t0) cc_final: 0.6670 (t0)
REVERT: B  521 ASP cc_start: 0.8187 (t0) cc_final: 0.7742 (t0)
REVERT: B  528 MET cc_start: 0.8596 (mtm) cc_final: 0.8314 (mtm)
REVERT: C   50 MET cc_start: 0.8809 (ppp) cc_final: 0.8435 (ppp)
REVERT: C   51 GLU cc_start: 0.8756 (tp30) cc_final: 0.8350 (tm-30)
REVERT: C   57 LEU cc_start: 0.8621 (mt) cc_final: 0.8398 (mt)
REVERT: F   22 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7556 (mtp180)
REVERT: F   34 GLN cc_start: 0.8650 (pt0) cc_final: 0.8171 (tp-100)
REVERT: F   38 ASP cc_start: 0.8615 (p0) cc_final: 0.8330 (p0)
REVERT: F   65 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.2019 (p90)
REVERT: F   93 ARG cc_start: 0.7287 (mtp180) cc_final: 0.6751 (mtp85)
REVERT: F   97 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: F  102 TYR cc_start: 0.8751 (t80) cc_final: 0.8421 (t80)
REVERT: E  220 PHE cc_start: 0.6953 (t80) cc_final: 0.6718 (t80)
  outliers start: 45
  outliers final: 34
  residues processed: 266
  average time/residue: 0.1069
  time to fit residues: 40.6197
Evaluate side-chains
  261 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 223
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  690 ILE
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   41 THR
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   94 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  211 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 67 optimal weight:    0.0670
   chunk 94 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 75 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 410 ASN
A 583 ASN
B 563 ASN
C  78 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.150508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119347 restraints weight = 21618.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.123031 restraints weight = 12128.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.125423 restraints weight = 8523.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.126899 restraints weight = 6894.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.127813 restraints weight = 6072.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11271  Z= 0.125
  Angle     :  0.660  14.503  15192  Z= 0.323
  Chirality :  0.042   0.178   1634
  Planarity :  0.004   0.049   1941
  Dihedral  :  4.458  19.471   1455
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.60 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.24), residues: 1318
  helix:  0.96 (0.21), residues: 617
  sheet: -2.15 (0.54), residues: 82
  loop : -1.07 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.020   0.001   TYR B 456 
 PHE   0.034   0.002   PHE F  29 
 TRP   0.028   0.002   TRP A 268 
 HIS   0.009   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11251)
  covalent geometry    : angle       0.65719 (15183)
  hydrogen bonds       : bond        0.03906 (  492)
  hydrogen bonds       : angle       4.55903 ( 1416)
  metal coordination   : bond        0.00832 (   20)
  metal coordination   : angle       2.50319 (    9)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 241
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.7785 (tpp) cc_final: 0.7420 (tpp)
REVERT: A  334 TYR cc_start: 0.8227 (t80) cc_final: 0.7642 (t80)
REVERT: A  347 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7077 (ptt-90)
REVERT: A  540 ILE cc_start: 0.8365 (pt) cc_final: 0.7881 (mt)
REVERT: A  625 ARG cc_start: 0.6780 (ttp80) cc_final: 0.6477 (tpt-90)
REVERT: B   22 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8116 (p90)
REVERT: B  165 LYS cc_start: 0.9083 (tppt) cc_final: 0.8619 (tppt)
REVERT: B  207 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6110 (ttp)
REVERT: B  227 GLU cc_start: 0.8658 (tp30) cc_final: 0.8434 (tt0)
REVERT: B  316 ASN cc_start: 0.6867 (t0) cc_final: 0.6660 (t0)
REVERT: B  521 ASP cc_start: 0.8180 (t0) cc_final: 0.7732 (t0)
REVERT: B  528 MET cc_start: 0.8593 (mtm) cc_final: 0.8357 (mtm)
REVERT: B  593 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7234 (mtp85)
REVERT: C   50 MET cc_start: 0.8740 (ppp) cc_final: 0.8371 (ppp)
REVERT: C   51 GLU cc_start: 0.8700 (tp30) cc_final: 0.8332 (tm-30)
REVERT: C   57 LEU cc_start: 0.8628 (mt) cc_final: 0.8427 (mt)
REVERT: C   91 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8121 (m110)
REVERT: F   22 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7432 (mtp180)
REVERT: F   34 GLN cc_start: 0.8528 (pt0) cc_final: 0.8027 (tp-100)
REVERT: F   38 ASP cc_start: 0.8577 (p0) cc_final: 0.8202 (p0)
REVERT: F   40 GLU cc_start: 0.8454 (tp30) cc_final: 0.8117 (tp30)
REVERT: F   65 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.1932 (p90)
REVERT: F   93 ARG cc_start: 0.7335 (mtp180) cc_final: 0.6791 (mtp85)
REVERT: F   97 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8135 (mt)
REVERT: F  102 TYR cc_start: 0.8720 (t80) cc_final: 0.8369 (t80)
REVERT: E  219 GLU cc_start: 0.7655 (pm20) cc_final: 0.7420 (pm20)
  outliers start: 42
  outliers final: 30
  residues processed: 267
  average time/residue: 0.0950
  time to fit residues: 36.3191
Evaluate side-chains
  259 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 223
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   94 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  211 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 123 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0670
   overall best weight:    1.2124

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 583 ASN
B 229 HIS
C  73 HIS
C  78 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.146737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114361 restraints weight = 21894.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118011 restraints weight = 12031.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.120375 restraints weight = 8422.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.121851 restraints weight = 6811.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.122763 restraints weight = 5991.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11271  Z= 0.145
  Angle     :  0.689  14.799  15192  Z= 0.335
  Chirality :  0.044   0.473   1634
  Planarity :  0.004   0.049   1941
  Dihedral  :  4.488  20.229   1455
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.16 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.23), residues: 1318
  helix:  0.95 (0.21), residues: 617
  sheet: -2.16 (0.54), residues: 82
  loop : -1.10 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 157 
 TYR   0.021   0.001   TYR F  43 
 PHE   0.033   0.002   PHE F  29 
 TRP   0.033   0.002   TRP A 268 
 HIS   0.011   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11251)
  covalent geometry    : angle       0.68605 (15183)
  hydrogen bonds       : bond        0.04014 (  492)
  hydrogen bonds       : angle       4.64825 ( 1416)
  metal coordination   : bond        0.01039 (   20)
  metal coordination   : angle       2.68343 (    9)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.8300 (mttt) cc_final: 0.8076 (mmmt)
REVERT: A  203 MET cc_start: 0.7814 (tpp) cc_final: 0.7452 (tpp)
REVERT: A  334 TYR cc_start: 0.8293 (t80) cc_final: 0.7741 (t80)
REVERT: A  625 ARG cc_start: 0.6736 (ttp80) cc_final: 0.6450 (tpt-90)
REVERT: B   22 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8195 (p90)
REVERT: B  165 LYS cc_start: 0.9105 (tppt) cc_final: 0.8660 (tppt)
REVERT: B  207 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6239 (ttp)
REVERT: B  227 GLU cc_start: 0.8730 (tp30) cc_final: 0.8469 (tt0)
REVERT: B  316 ASN cc_start: 0.7037 (t0) cc_final: 0.6813 (t0)
REVERT: B  528 MET cc_start: 0.8630 (mtm) cc_final: 0.8386 (mtm)
REVERT: B  593 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7203 (mtp85)
REVERT: C   50 MET cc_start: 0.8778 (ppp) cc_final: 0.8436 (ppp)
REVERT: C   51 GLU cc_start: 0.8762 (tp30) cc_final: 0.8392 (tm-30)
REVERT: C   57 LEU cc_start: 0.8675 (mt) cc_final: 0.8407 (mt)
REVERT: C   91 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8203 (m110)
REVERT: F   22 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7381 (mtp180)
REVERT: F   34 GLN cc_start: 0.8576 (pt0) cc_final: 0.8226 (tp-100)
REVERT: F   65 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.2007 (p90)
REVERT: F   93 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6894 (mtp85)
REVERT: F   97 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: F  102 TYR cc_start: 0.8771 (t80) cc_final: 0.8398 (t80)
REVERT: E  239 VAL cc_start: 0.8586 (t) cc_final: 0.8364 (m)
  outliers start: 42
  outliers final: 34
  residues processed: 248
  average time/residue: 0.0956
  time to fit residues: 33.5584
Evaluate side-chains
  258 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 219
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  371 TYR
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  435 MET
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  574 ILE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  523 CYS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   22 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   70 ASP
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue   91 ASN
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain F residue   65 TYR
Chi-restraints excluded: chain F residue   94 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  211 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 48 optimal weight:    0.3980
   chunk 108 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 128 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 583 ASN
B 229 HIS
C  73 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.147767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116345 restraints weight = 21818.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119935 restraints weight = 12099.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.122297 restraints weight = 8511.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.123273 restraints weight = 6903.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.124591 restraints weight = 6212.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  11271  Z= 0.129
  Angle     :  0.678  14.649  15192  Z= 0.330
  Chirality :  0.043   0.447   1634
  Planarity :  0.004   0.052   1941
  Dihedral  :  4.422  19.669   1455
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.65 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.23), residues: 1318
  helix:  0.97 (0.21), residues: 619
  sheet: -2.02 (0.55), residues: 82
  loop : -1.09 (0.26), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 157 
 TYR   0.023   0.001   TYR F  43 
 PHE   0.032   0.002   PHE F  95 
 TRP   0.027   0.002   TRP A 268 
 HIS   0.012   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11251)
  covalent geometry    : angle       0.67607 (15183)
  hydrogen bonds       : bond        0.03912 (  492)
  hydrogen bonds       : angle       4.59555 ( 1416)
  metal coordination   : bond        0.00836 (   20)
  metal coordination   : angle       2.41828 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1828.66 seconds
wall clock time: 32 minutes 27.82 seconds (1947.82 seconds total)