Starting phenix.real_space_refine
on Sat Aug 23 01:08:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuv_50779/08_2025/9fuv_50779.cif"
  }
  resolution = 4.0
  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=   0.008
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 1.69, per 1000 atoms: 0.19
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (116.96, 101.32, 136.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 0.68
  Conformation dependent library (CDL) restraints added in 337.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      68.4% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.888A  pdb=" N   ILE A  35 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   MET A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.549A  pdb=" N   ASP A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 111
      removed outlier: 3.943A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 3.554A  pdb=" N   GLY A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
      removed outlier: 3.974A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 164
      removed outlier: 3.852A  pdb=" N   GLU A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 213
      Proline residue:  A 176  - end of helix
      removed outlier: 3.637A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.553A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 269
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 281 through 323
      removed outlier: 4.086A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.592A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.535A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.852A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 4.086A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.764A  pdb=" N   THR A 472 " --> pdb=" O   GLY A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 23 through 55
      removed outlier: 4.419A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU B  48 " --> pdb=" O   MET B  44 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 110
      removed outlier: 4.188A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.970A  pdb=" N   THR B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 129
    Processing helix  chain 'B' and resid 129 through 147
    Processing helix  chain 'B' and resid 147 through 164
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 173 through 213
      removed outlier: 4.111A  pdb=" N   ILE B 177 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.898A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 281 through 323
      removed outlier: 3.785A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 4.239A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B 313 " --> pdb=" O   GLN B 309 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ALA B 314 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   CYS B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 391
      removed outlier: 3.837A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
      removed outlier: 3.669A  pdb=" N   ILE B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU B 451 " --> pdb=" O   ARG B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 4.363A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.528A  pdb=" N   GLU A 343 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 3.510A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 422 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 342 through 345
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.123A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU B 547 " --> pdb=" O   THR B 371 " (cutoff:3.500A)

    557 hydrogen bonds defined for protein.
    1650 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: 1.22

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2867
        1.34 -     1.45: 1039
        1.45 -     1.57: 4940
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   VAL A  65 "
       pdb=" CA  VAL A  65 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.23e+00
  bond pdb=" N   VAL B  63 "
       pdb=" CA  VAL B  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.29e-02 6.01e+03 7.39e+00
  bond pdb=" N   VAL B 356 "
       pdb=" CA  VAL B 356 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.23e-02 6.61e+03 7.30e+00
  bond pdb=" N   VAL A  63 "
       pdb=" CA  VAL A  63 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.26e-02 6.30e+03 7.16e+00
  bond pdb=" N   THR B 472 "
       pdb=" CA  THR B 472 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.22e-02 6.72e+03 7.11e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 11296
        1.23 -     2.47: 629
        2.47 -     3.70: 120
        3.70 -     4.93: 34
        4.93 -     6.16: 13
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   ALA B 358 "
        pdb=" CA  ALA B 358 "
        pdb=" C   ALA B 358 "
      ideal   model   delta    sigma   weight residual
     113.16  108.07    5.09 1.24e+00 6.50e-01 1.69e+01
  angle pdb=" C   THR B 472 "
        pdb=" CA  THR B 472 "
        pdb=" CB  THR B 472 "
      ideal   model   delta    sigma   weight residual
     109.89  103.73    6.16 1.60e+00 3.91e-01 1.48e+01
  angle pdb=" N   ASP B 341 "
        pdb=" CA  ASP B 341 "
        pdb=" C   ASP B 341 "
      ideal   model   delta    sigma   weight residual
     109.59  115.16   -5.57 1.47e+00 4.63e-01 1.44e+01
  angle pdb=" N   GLU B 327 "
        pdb=" CA  GLU B 327 "
        pdb=" CB  GLU B 327 "
      ideal   model   delta    sigma   weight residual
     109.19  114.76   -5.57 1.54e+00 4.22e-01 1.31e+01
  angle pdb=" N   LEU B 125 "
        pdb=" CA  LEU B 125 "
        pdb=" C   LEU B 125 "
      ideal   model   delta    sigma   weight residual
     111.36  107.53    3.83 1.09e+00 8.42e-01 1.24e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 4614
       16.94 -    33.87: 610
       33.87 -    50.81: 184
       50.81 -    67.74: 37
       67.74 -    84.68: 9
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  TRP A  17 "
           pdb=" C   TRP A  17 "
           pdb=" N   PRO A  18 "
           pdb=" CA  PRO A  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  PHE A 272 "
           pdb=" C   PHE A 272 "
           pdb=" N   PRO A 273 "
           pdb=" CA  PRO A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  PHE A  13 "
           pdb=" C   PHE A  13 "
           pdb=" N   ARG A  14 "
           pdb=" CA  ARG A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.12   19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1034
       0.036 -    0.073: 286
       0.073 -    0.109: 90
       0.109 -    0.146: 21
       0.146 -    0.182: 9
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  LEU B 125 "
            pdb=" N   LEU B 125 "
            pdb=" C   LEU B 125 "
            pdb=" CB  LEU B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.27e-01
  chirality pdb=" CA  VAL A  63 "
            pdb=" N   VAL A  63 "
            pdb=" C   VAL A  63 "
            pdb=" CB  VAL A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" CB  VAL A  63 "
            pdb=" CA  VAL A  63 "
            pdb=" CG1 VAL A  63 "
            pdb=" CG2 VAL A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.02e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 296 "    0.051 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO A 297 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 297 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 297 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  49 "    0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO B  50 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 133 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.19e+00
        pdb=" C   GLU B 133 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLU B 133 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN B 134 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 866
        2.73 -     3.27: 10297
        3.27 -     3.82: 15382
        3.82 -     4.36: 17502
        4.36 -     4.90: 28205
  Nonbonded interactions: 72252
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" N   ASN A 468 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" O   GLY A 282 "
            pdb=" OG1 THR A 285 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 202 "
            pdb=" OG1 THR A 205 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NH2 ARG B 102 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ARG A 377 "
            pdb=" NE  ARG A 377 "
     model   vdw
     2.250 3.120
  ... (remaining 72247 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             5.130
  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:          0.250
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.010
  Find NCS groups from input model:        0.110
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
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      :  0.004   0.037   8950  Z= 0.214
  Angle     :  0.690   6.163  12092  Z= 0.407
  Chirality :  0.041   0.182   1440
  Planarity :  0.005   0.076   1532
  Dihedral  : 17.155  84.677   3326
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.03 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 31.30 %
    Favored  : 68.08 %
  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 aren not related in a simple way.
  whole: -0.04 (0.25), residues: 1134
  helix:  0.93 (0.20), residues: 702
  sheet: -1.16 (0.75), residues: 56
  loop : -1.65 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 377 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.014   0.002   PHE A  56 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.006   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8950)
  covalent geometry    : angle       0.68965 (12092)
  hydrogen bonds       : bond        0.15279 (  557)
  hydrogen bonds       : angle       6.71115 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8210 (tpp) cc_final: 0.7934 (ttt)
REVERT: A  149 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7784 (mm-30)
REVERT: A  295 MET cc_start: 0.8203 (ttm) cc_final: 0.7915 (ttm)
REVERT: A  312 MET cc_start: 0.8618 (mmm) cc_final: 0.8100 (mmm)
REVERT: A  495 LEU cc_start: 0.9092 (mm) cc_final: 0.8859 (mm)
REVERT: B   98 MET cc_start: 0.8232 (ppp) cc_final: 0.7793 (tmm)
REVERT: B  456 MET cc_start: 0.9047 (ttp) cc_final: 0.8841 (ptm)
REVERT: B  481 LEU cc_start: 0.8859 (mt) cc_final: 0.8525 (pt)
REVERT: B  495 LEU cc_start: 0.9042 (tt) cc_final: 0.8806 (tt)
  outliers start: 6
  outliers final: 3
  residues processed: 167
  average time/residue: 0.0730
  time to fit residues: 17.8046
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue  470 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.093911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071056 restraints weight = 30180.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.073265 restraints weight = 16927.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.074811 restraints weight = 11535.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075831 restraints weight = 8850.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.076450 restraints weight = 7424.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   8950  Z= 0.281
  Angle     :  0.767   9.666  12092  Z= 0.403
  Chirality :  0.045   0.159   1440
  Planarity :  0.005   0.042   1532
  Dihedral  :  5.479  53.612   1243
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.20 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 30.48 %
    Favored  : 63.74 %
  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 aren not related in a simple way.
  whole: -0.12 (0.25), residues: 1134
  helix:  0.74 (0.19), residues: 726
  sheet: -0.56 (0.75), residues: 56
  loop : -1.67 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 101 
 TYR   0.038   0.002   TYR A 439 
 PHE   0.027   0.003   PHE A  23 
 TRP   0.008   0.002   TRP A  91 
 HIS   0.009   0.002   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 8950)
  covalent geometry    : angle       0.76653 (12092)
  hydrogen bonds       : bond        0.05375 (  557)
  hydrogen bonds       : angle       5.35518 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 139
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (mp)
REVERT: A   98 MET cc_start: 0.8858 (tpp) cc_final: 0.8406 (tpp)
REVERT: A  111 MET cc_start: 0.8591 (tpp) cc_final: 0.8331 (ttt)
REVERT: A  209 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8168 (mp10)
REVERT: A  295 MET cc_start: 0.8175 (ttm) cc_final: 0.7878 (ttm)
REVERT: A  349 PHE cc_start: 0.8121 (t80) cc_final: 0.7913 (t80)
REVERT: A  495 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8788 (mm)
REVERT: B   98 MET cc_start: 0.8865 (ppp) cc_final: 0.8324 (tmm)
REVERT: B  100 MET cc_start: 0.8863 (mmp) cc_final: 0.8583 (tpp)
REVERT: B  325 GLU cc_start: 0.8041 (pm20) cc_final: 0.7771 (pm20)
REVERT: B  388 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9309 (tp)
REVERT: B  481 LEU cc_start: 0.8918 (mt) cc_final: 0.8582 (pt)
REVERT: B  562 HIS cc_start: 0.8115 (p-80) cc_final: 0.7840 (p-80)
  outliers start: 56
  outliers final: 33
  residues processed: 183
  average time/residue: 0.0844
  time to fit residues: 22.5056
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 GLN
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 579 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.094966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.071755 restraints weight = 30009.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.073901 restraints weight = 16988.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.075467 restraints weight = 11673.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.076521 restraints weight = 9027.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.077174 restraints weight = 7553.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8950  Z= 0.207
  Angle     :  0.692   9.011  12092  Z= 0.360
  Chirality :  0.043   0.175   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  5.289  57.392   1241
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.76 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 29.34 %
    Favored  : 63.84 %
  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 aren not related in a simple way.
  whole: -0.12 (0.25), residues: 1134
  helix:  0.83 (0.19), residues: 726
  sheet: -1.42 (0.67), residues: 64
  loop : -1.70 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  14 
 TYR   0.028   0.002   TYR A 439 
 PHE   0.020   0.002   PHE A 392 
 TRP   0.006   0.001   TRP A 165 
 HIS   0.006   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8950)
  covalent geometry    : angle       0.69199 (12092)
  hydrogen bonds       : bond        0.04937 (  557)
  hydrogen bonds       : angle       4.96013 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 145
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8855 (tpp) cc_final: 0.8262 (tpp)
REVERT: A  111 MET cc_start: 0.8538 (tpp) cc_final: 0.8319 (ttt)
REVERT: A  209 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8141 (mp10)
REVERT: A  295 MET cc_start: 0.8164 (ttm) cc_final: 0.7830 (ttm)
REVERT: A  349 PHE cc_start: 0.8040 (t80) cc_final: 0.7819 (t80)
REVERT: A  495 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8796 (mm)
REVERT: B   98 MET cc_start: 0.8906 (ppp) cc_final: 0.8351 (tmm)
REVERT: B  107 HIS cc_start: 0.8653 (OUTLIER) cc_final: 0.8126 (t-90)
REVERT: B  133 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8018 (tm-30)
REVERT: B  149 GLU cc_start: 0.8184 (tp30) cc_final: 0.7617 (mm-30)
REVERT: B  388 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9320 (tp)
REVERT: B  486 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8772 (mtt90)
REVERT: B  562 HIS cc_start: 0.8118 (p-80) cc_final: 0.7843 (p-80)
  outliers start: 66
  outliers final: 44
  residues processed: 197
  average time/residue: 0.0833
  time to fit residues: 23.9840
Evaluate side-chains
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 130
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 89 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 430 ASN
B 436 ASN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.097655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.074822 restraints weight = 30136.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.077102 restraints weight = 16946.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.078681 restraints weight = 11548.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.079683 restraints weight = 8878.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.080434 restraints weight = 7481.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.143
  Angle     :  0.651  10.900  12092  Z= 0.331
  Chirality :  0.042   0.197   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  5.033  51.287   1241
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.67 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 30.89 %
    Favored  : 63.02 %
  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 aren not related in a simple way.
  whole:  0.09 (0.25), residues: 1134
  helix:  0.95 (0.19), residues: 732
  sheet: -1.41 (0.66), residues: 64
  loop : -1.55 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  14 
 TYR   0.018   0.001   TYR A 439 
 PHE   0.015   0.002   PHE A  56 
 TRP   0.005   0.001   TRP A 165 
 HIS   0.012   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8950)
  covalent geometry    : angle       0.65105 (12092)
  hydrogen bonds       : bond        0.04438 (  557)
  hydrogen bonds       : angle       4.59055 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 153
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.6119 (mmt) cc_final: 0.5761 (mmt)
REVERT: A   98 MET cc_start: 0.8903 (tpp) cc_final: 0.8547 (tpp)
REVERT: A  107 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7512 (t-90)
REVERT: A  111 MET cc_start: 0.8420 (tpp) cc_final: 0.8140 (ttt)
REVERT: A  295 MET cc_start: 0.8040 (ttm) cc_final: 0.7745 (ttm)
REVERT: A  312 MET cc_start: 0.8758 (tpp) cc_final: 0.8558 (tpp)
REVERT: A  349 PHE cc_start: 0.7947 (t80) cc_final: 0.7730 (t80)
REVERT: A  487 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8583 (tp40)
REVERT: A  495 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8750 (mm)
REVERT: B   17 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.6517 (t60)
REVERT: B   98 MET cc_start: 0.8762 (ppp) cc_final: 0.8039 (tmm)
REVERT: B  107 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.7995 (t-90)
REVERT: B  133 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: B  149 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7695 (mp0)
REVERT: B  196 MET cc_start: 0.8876 (mtp) cc_final: 0.8580 (mtp)
REVERT: B  374 LEU cc_start: 0.8963 (mm) cc_final: 0.8605 (tp)
REVERT: B  388 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9297 (tp)
REVERT: B  439 TYR cc_start: 0.8277 (t80) cc_final: 0.7998 (t80)
REVERT: B  481 LEU cc_start: 0.8364 (mm) cc_final: 0.7994 (mt)
REVERT: B  486 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8688 (mtt90)
  outliers start: 59
  outliers final: 40
  residues processed: 199
  average time/residue: 0.0827
  time to fit residues: 24.0168
Evaluate side-chains
  186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 137
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  524 ASP
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 111 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 99 optimal weight:    0.2980
   chunk 49 optimal weight:    0.0980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
** B 485 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 = 0.3692 r_free = 0.3692 target = 0.099503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.077045 restraints weight = 29701.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079372 restraints weight = 16573.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.080963 restraints weight = 11186.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.082034 restraints weight = 8519.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.082747 restraints weight = 7078.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.129
  Angle     :  0.633  10.848  12092  Z= 0.319
  Chirality :  0.042   0.181   1440
  Planarity :  0.004   0.036   1532
  Dihedral  :  4.903  55.560   1241
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.14 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 29.55 %
    Favored  : 64.05 %
  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 aren not related in a simple way.
  whole:  0.27 (0.25), residues: 1134
  helix:  1.12 (0.19), residues: 732
  sheet: -1.43 (0.65), residues: 64
  loop : -1.54 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 102 
 TYR   0.016   0.001   TYR A 439 
 PHE   0.014   0.001   PHE A  56 
 TRP   0.005   0.001   TRP A 165 
 HIS   0.012   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8950)
  covalent geometry    : angle       0.63266 (12092)
  hydrogen bonds       : bond        0.04221 (  557)
  hydrogen bonds       : angle       4.40705 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 158
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8906 (tpp) cc_final: 0.8156 (tpp)
REVERT: A  107 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7486 (t-90)
REVERT: A  295 MET cc_start: 0.7938 (ttm) cc_final: 0.7652 (ttm)
REVERT: A  326 GLN cc_start: 0.3584 (OUTLIER) cc_final: 0.3066 (tt0)
REVERT: A  487 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8531 (tp40)
REVERT: A  495 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8736 (mm)
REVERT: B   17 TRP cc_start: 0.6671 (OUTLIER) cc_final: 0.6455 (t60)
REVERT: B   98 MET cc_start: 0.8653 (ppp) cc_final: 0.8337 (tmm)
REVERT: B  107 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.7972 (t-90)
REVERT: B  133 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8039 (tm-30)
REVERT: B  149 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7646 (mp0)
REVERT: B  196 MET cc_start: 0.8845 (mtp) cc_final: 0.8610 (mtp)
REVERT: B  374 LEU cc_start: 0.8909 (mm) cc_final: 0.8609 (tp)
REVERT: B  388 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9287 (tp)
REVERT: B  481 LEU cc_start: 0.8493 (mm) cc_final: 0.8118 (mt)
REVERT: B  486 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8566 (mtt90)
  outliers start: 62
  outliers final: 41
  residues processed: 204
  average time/residue: 0.0849
  time to fit residues: 25.1138
Evaluate side-chains
  191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 140
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   61 ARG
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 TRP
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  436 ASN
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.099458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.076892 restraints weight = 29816.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.079208 restraints weight = 16783.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.080762 restraints weight = 11399.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.081879 restraints weight = 8754.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.082559 restraints weight = 7266.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.133
  Angle     :  0.655  12.866  12092  Z= 0.328
  Chirality :  0.042   0.176   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.877  57.317   1241
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.32 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 31.30 %
    Favored  : 62.19 %
  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 aren not related in a simple way.
  whole:  0.41 (0.25), residues: 1134
  helix:  1.24 (0.19), residues: 732
  sheet: -1.45 (0.65), residues: 64
  loop : -1.48 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 377 
 TYR   0.024   0.001   TYR A 439 
 PHE   0.014   0.002   PHE A  23 
 TRP   0.004   0.001   TRP A  91 
 HIS   0.013   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8950)
  covalent geometry    : angle       0.65455 (12092)
  hydrogen bonds       : bond        0.04199 (  557)
  hydrogen bonds       : angle       4.31802 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 147
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8893 (tpp) cc_final: 0.8189 (tpp)
REVERT: A  107 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7431 (t-90)
REVERT: A  149 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: A  295 MET cc_start: 0.7933 (ttm) cc_final: 0.7633 (ttm)
REVERT: A  326 GLN cc_start: 0.3675 (OUTLIER) cc_final: 0.3153 (tt0)
REVERT: A  495 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8741 (mm)
REVERT: B   98 MET cc_start: 0.8665 (ppp) cc_final: 0.8372 (tmm)
REVERT: B  107 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7982 (t-90)
REVERT: B  133 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7710 (tm-30)
REVERT: B  149 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7596 (mm-30)
REVERT: B  196 MET cc_start: 0.8898 (mtp) cc_final: 0.8657 (mtp)
REVERT: B  374 LEU cc_start: 0.8991 (mm) cc_final: 0.8632 (tp)
REVERT: B  388 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9263 (tp)
REVERT: B  481 LEU cc_start: 0.8525 (mm) cc_final: 0.8211 (mt)
  outliers start: 63
  outliers final: 45
  residues processed: 196
  average time/residue: 0.0867
  time to fit residues: 24.5215
Evaluate side-chains
  190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 138
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  436 ASN
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 88 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0020
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.099834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.077308 restraints weight = 29993.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.079612 restraints weight = 16884.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.081224 restraints weight = 11461.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.082305 restraints weight = 8751.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.083076 restraints weight = 7275.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8950  Z= 0.130
  Angle     :  0.645  11.493  12092  Z= 0.323
  Chirality :  0.042   0.151   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.884  58.639   1241
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.41 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 31.10 %
    Favored  : 62.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.25), residues: 1134
  helix:  1.32 (0.19), residues: 730
  sheet: -1.55 (0.64), residues: 64
  loop : -1.59 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 488 
 TYR   0.011   0.001   TYR A 163 
 PHE   0.013   0.001   PHE A  23 
 TRP   0.003   0.001   TRP A 165 
 HIS   0.014   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8950)
  covalent geometry    : angle       0.64454 (12092)
  hydrogen bonds       : bond        0.04132 (  557)
  hydrogen bonds       : angle       4.26132 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 145
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8875 (tpp) cc_final: 0.8147 (tpp)
REVERT: A  107 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7483 (t-90)
REVERT: A  149 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7612 (mm-30)
REVERT: A  163 TYR cc_start: 0.8782 (m-80) cc_final: 0.8539 (m-80)
REVERT: A  295 MET cc_start: 0.7928 (ttm) cc_final: 0.7630 (ttm)
REVERT: A  326 GLN cc_start: 0.3753 (OUTLIER) cc_final: 0.3176 (tt0)
REVERT: A  495 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8715 (mm)
REVERT: B   98 MET cc_start: 0.8611 (ppp) cc_final: 0.8356 (tmm)
REVERT: B  107 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8003 (t-90)
REVERT: B  133 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7803 (tm-30)
REVERT: B  149 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7592 (mm-30)
REVERT: B  196 MET cc_start: 0.8880 (mtp) cc_final: 0.8654 (mtp)
REVERT: B  374 LEU cc_start: 0.8997 (mm) cc_final: 0.8669 (tp)
REVERT: B  388 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9250 (tp)
REVERT: B  465 LYS cc_start: 0.8338 (pttt) cc_final: 0.7906 (pptt)
REVERT: B  481 LEU cc_start: 0.8541 (mm) cc_final: 0.8216 (mt)
  outliers start: 60
  outliers final: 44
  residues processed: 191
  average time/residue: 0.0726
  time to fit residues: 21.0711
Evaluate side-chains
  188 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 137
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  436 ASN
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 88 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.098305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075682 restraints weight = 29699.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.077956 restraints weight = 16752.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.079535 restraints weight = 11397.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.080602 restraints weight = 8737.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.081366 restraints weight = 7258.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8950  Z= 0.158
  Angle     :  0.662  11.688  12092  Z= 0.334
  Chirality :  0.042   0.159   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.922  59.154   1241
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.59 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 30.89 %
    Favored  : 62.40 %
  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 aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1134
  helix:  1.31 (0.19), residues: 718
  sheet: -2.44 (0.65), residues: 44
  loop : -1.34 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 517 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.018   0.002   PHE A  23 
 TRP   0.008   0.001   TRP A  17 
 HIS   0.014   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8950)
  covalent geometry    : angle       0.66190 (12092)
  hydrogen bonds       : bond        0.04245 (  557)
  hydrogen bonds       : angle       4.35201 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 142
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8899 (tpp) cc_final: 0.8120 (tpp)
REVERT: A  107 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7546 (t-90)
REVERT: A  149 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7643 (mm-30)
REVERT: A  163 TYR cc_start: 0.8883 (m-80) cc_final: 0.8578 (m-80)
REVERT: A  295 MET cc_start: 0.7917 (ttm) cc_final: 0.7618 (ttm)
REVERT: A  326 GLN cc_start: 0.4038 (OUTLIER) cc_final: 0.3466 (tt0)
REVERT: A  487 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8554 (mm-40)
REVERT: A  495 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8731 (mm)
REVERT: B   98 MET cc_start: 0.8698 (ppp) cc_final: 0.8437 (tmm)
REVERT: B  107 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8104 (t-90)
REVERT: B  133 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7714 (tm-30)
REVERT: B  149 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7642 (mm-30)
REVERT: B  388 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9240 (tp)
REVERT: B  481 LEU cc_start: 0.8582 (mm) cc_final: 0.8178 (mt)
REVERT: B  486 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8608 (mtt90)
  outliers start: 65
  outliers final: 47
  residues processed: 194
  average time/residue: 0.0781
  time to fit residues: 22.5306
Evaluate side-chains
  197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 141
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  436 ASN
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0270
   chunk 105 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
A 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.099873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.077441 restraints weight = 29542.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.079752 restraints weight = 16531.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.081358 restraints weight = 11183.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.082460 restraints weight = 8527.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.083180 restraints weight = 7058.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.133
  Angle     :  0.679  13.175  12092  Z= 0.335
  Chirality :  0.041   0.152   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.881  58.838   1241
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.59 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 32.85 %
    Favored  : 61.67 %
  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 aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1134
  helix:  1.33 (0.19), residues: 718
  sheet: -2.42 (0.63), residues: 44
  loop : -1.36 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 517 
 TYR   0.010   0.001   TYR A 163 
 PHE   0.012   0.001   PHE A  23 
 TRP   0.003   0.000   TRP A  91 
 HIS   0.016   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8950)
  covalent geometry    : angle       0.67939 (12092)
  hydrogen bonds       : bond        0.04119 (  557)
  hydrogen bonds       : angle       4.28619 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 148
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8836 (tpp) cc_final: 0.8084 (tpp)
REVERT: A  107 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7522 (t-90)
REVERT: A  149 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A  163 TYR cc_start: 0.8848 (m-80) cc_final: 0.8603 (m-80)
REVERT: A  295 MET cc_start: 0.7926 (ttm) cc_final: 0.7624 (ttm)
REVERT: A  326 GLN cc_start: 0.4083 (OUTLIER) cc_final: 0.3567 (tt0)
REVERT: A  487 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8544 (tp40)
REVERT: A  495 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8708 (mm)
REVERT: B   98 MET cc_start: 0.8608 (ppp) cc_final: 0.8401 (tmm)
REVERT: B  107 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8066 (t-90)
REVERT: B  133 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7735 (tm-30)
REVERT: B  149 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7642 (mm-30)
REVERT: B  388 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9238 (tp)
REVERT: B  465 LYS cc_start: 0.8417 (pttt) cc_final: 0.8038 (pptt)
REVERT: B  481 LEU cc_start: 0.8575 (mm) cc_final: 0.8245 (mt)
  outliers start: 53
  outliers final: 43
  residues processed: 190
  average time/residue: 0.0748
  time to fit residues: 21.1725
Evaluate side-chains
  192 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 141
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.096585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.073772 restraints weight = 29817.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.075972 restraints weight = 16954.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.077522 restraints weight = 11612.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.078459 restraints weight = 8934.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.079179 restraints weight = 7544.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8950  Z= 0.190
  Angle     :  0.727  13.760  12092  Z= 0.363
  Chirality :  0.043   0.144   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  5.019  55.765   1241
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.94 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 32.33 %
    Favored  : 61.88 %
  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 aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1134
  helix:  1.23 (0.19), residues: 718
  sheet: -2.01 (0.71), residues: 46
  loop : -1.37 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 517 
 TYR   0.015   0.001   TYR A 163 
 PHE   0.024   0.002   PHE A  23 
 TRP   0.014   0.001   TRP A  17 
 HIS   0.015   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8950)
  covalent geometry    : angle       0.72660 (12092)
  hydrogen bonds       : bond        0.04490 (  557)
  hydrogen bonds       : angle       4.48806 ( 1650)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 138
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8846 (tpp) cc_final: 0.8030 (tpp)
REVERT: A  107 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7630 (t-90)
REVERT: A  149 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: A  158 ILE cc_start: 0.8659 (mm) cc_final: 0.8316 (tp)
REVERT: A  163 TYR cc_start: 0.8984 (m-80) cc_final: 0.8606 (m-80)
REVERT: A  295 MET cc_start: 0.7929 (ttm) cc_final: 0.7646 (ttm)
REVERT: A  465 LYS cc_start: 0.8309 (pttm) cc_final: 0.7407 (ptpt)
REVERT: A  487 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8579 (tp40)
REVERT: A  495 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: B   98 MET cc_start: 0.8761 (ppp) cc_final: 0.8392 (tmm)
REVERT: B  107 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8089 (t-90)
REVERT: B  133 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7571 (tm-30)
REVERT: B  149 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7685 (mm-30)
REVERT: B  374 LEU cc_start: 0.9004 (mm) cc_final: 0.8585 (tp)
REVERT: B  388 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9229 (tp)
REVERT: B  481 LEU cc_start: 0.8626 (mm) cc_final: 0.8206 (mt)
REVERT: B  486 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8660 (mtt90)
  outliers start: 56
  outliers final: 45
  residues processed: 183
  average time/residue: 0.0776
  time to fit residues: 21.2553
Evaluate side-chains
  186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 133
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue   17 TRP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  209 GLN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  107 HIS
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  446 SER
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  464 ASN
Chi-restraints excluded: chain B residue  486 ARG
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0670
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.099573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.077013 restraints weight = 29347.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.079273 restraints weight = 16579.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.080764 restraints weight = 11321.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.081862 restraints weight = 8767.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.082472 restraints weight = 7296.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.133
  Angle     :  0.696  13.262  12092  Z= 0.340
  Chirality :  0.042   0.153   1440
  Planarity :  0.004   0.070   1532
  Dihedral  :  4.879  56.654   1241
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.41 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 32.85 %
    Favored  : 61.78 %
  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 aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1134
  helix:  1.39 (0.19), residues: 712
  sheet: -1.98 (0.69), residues: 46
  loop : -1.40 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 517 
 TYR   0.010   0.001   TYR A 163 
 PHE   0.014   0.002   PHE A 429 
 TRP   0.003   0.001   TRP A  91 
 HIS   0.017   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8950)
  covalent geometry    : angle       0.69560 (12092)
  hydrogen bonds       : bond        0.04173 (  557)
  hydrogen bonds       : angle       4.26690 ( 1650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1816.07 seconds
wall clock time: 32 minutes 14.99 seconds (1934.99 seconds total)