Starting phenix.real_space_refine
on Sat May 10 23:27:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j17_61070/05_2025/9j17_61070.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.047
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      52      5.16       5
     C    4588      2.51       5
     N    1134      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7052
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3510
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'ZEA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.41, per 1000 atoms: 0.91
  Number of scatterers: 7052
  At special positions: 0
  Unit cell: (78.1, 115.5, 78.1, 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      52     16.00
     O    1278      8.00
     N    1134      7.00
     C    4588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " distance=2.03

  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: 1.79
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1680

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      62.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 18
      removed outlier: 3.628A  pdb=" N   HIS A  17 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 39 through 55
    Processing helix  chain 'A' and resid 56 through 67
      removed outlier: 4.000A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
    Processing helix  chain 'A' and resid 95 through 128
      removed outlier: 3.583A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   GLY A 120 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ALA A 123 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 158 through 179
      removed outlier: 3.588A  pdb=" N   ALA A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 190 through 208
      removed outlier: 3.787A  pdb=" N   ARG A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LEU A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 264
      removed outlier: 3.724A  pdb=" N   LEU A 254 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 286
    Processing helix  chain 'A' and resid 298 through 310
      removed outlier: 4.695A  pdb=" N   LYS A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
      removed outlier: 4.026A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   TYR A 354 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 387
      removed outlier: 3.650A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 379 " --> pdb=" O   TYR A 375 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLY A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ALA A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.769A  pdb=" N   LEU A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 438 through 451
      removed outlier: 3.885A  pdb=" N   GLY A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.798A  pdb=" N   ILE A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 477
      removed outlier: 3.992A  pdb=" N   THR A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 479 through 494
      removed outlier: 3.960A  pdb=" N   GLY A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 489 " --> pdb=" O   ILE A 485 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 18
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 39 through 55
    Processing helix  chain 'B' and resid 56 through 67
      removed outlier: 4.000A  pdb=" N   ALA B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP B  67 " --> pdb=" O   ASN B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 95 through 128
      removed outlier: 3.583A  pdb=" N   VAL B 110 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   GLY B 120 " --> pdb=" O   SER B 116 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B 121 " --> pdb=" O   ALA B 117 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   ALA B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA B 128 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
    Processing helix  chain 'B' and resid 158 through 179
      removed outlier: 3.587A  pdb=" N   ALA B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 190 through 208
      removed outlier: 3.787A  pdb=" N   ARG B 194 " --> pdb=" O   PRO B 190 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU B 195 " --> pdb=" O   GLN B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 264
      removed outlier: 3.724A  pdb=" N   LEU B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 286
    Processing helix  chain 'B' and resid 298 through 310
      removed outlier: 4.695A  pdb=" N   LYS B 310 " --> pdb=" O   ASN B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356
      removed outlier: 4.026A  pdb=" N   GLY B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   TYR B 354 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 387
      removed outlier: 3.649A  pdb=" N   VAL B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA B 379 " --> pdb=" O   TYR B 375 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLY B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ALA B 387 " --> pdb=" O   VAL B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.769A  pdb=" N   LEU B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 438 through 451
      removed outlier: 3.884A  pdb=" N   GLY B 451 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.798A  pdb=" N   ILE B 456 " --> pdb=" O   VAL B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 477
      removed outlier: 3.991A  pdb=" N   THR B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
      Proline residue:  B 475  - end of helix
    Processing helix  chain 'B' and resid 479 through 494
      removed outlier: 3.960A  pdb=" N   GLY B 483 " --> pdb=" O   SER B 479 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 489 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135
      removed outlier: 4.121A  pdb=" N   ALA A 135 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA A 394 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135
      removed outlier: 4.121A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B 394 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220

    346 hydrogen bonds defined for protein.
    1002 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: 1.79

  Time building geometry restraints manager: 2.09 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: 2180
        1.34 -     1.46: 1271
        1.46 -     1.57: 3651
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 7192
  Sorted by residual:
  bond pdb=" C4  ZEA B 601 "
       pdb=" C5  ZEA B 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.457 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C4  ZEA A 601 "
       pdb=" C5  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.456 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" C5  ZEA A 601 "
       pdb=" C6  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.410  1.463 -0.053 2.00e-02 2.50e+03 7.02e+00
  bond pdb=" C5  ZEA B 601 "
       pdb=" C6  ZEA B 601 "
    ideal  model  delta    sigma   weight residual
    1.410  1.463 -0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" C8  ZEA A 601 "
       pdb=" N9  ZEA A 601 "
    ideal  model  delta    sigma   weight residual
    1.303  1.354 -0.051 2.00e-02 2.50e+03 6.54e+00
  ... (remaining 7187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.05: 9698
        5.05 -    10.11: 42
       10.11 -    15.16: 8
       15.16 -    20.22: 6
       20.22 -    25.27: 6
  Bond angle restraints: 9760
  Sorted by residual:
  angle pdb=" N   ALA A 145 "
        pdb=" CA  ALA A 145 "
        pdb=" C   ALA A 145 "
      ideal   model   delta    sigma   weight residual
     111.33  134.27  -22.94 1.21e+00 6.83e-01 3.59e+02
  angle pdb=" N   ALA B 145 "
        pdb=" CA  ALA B 145 "
        pdb=" C   ALA B 145 "
      ideal   model   delta    sigma   weight residual
     111.33  134.26  -22.93 1.21e+00 6.83e-01 3.59e+02
  angle pdb=" N   ALA A 231 "
        pdb=" CA  ALA A 231 "
        pdb=" C   ALA A 231 "
      ideal   model   delta    sigma   weight residual
     109.96   84.69   25.27 1.50e+00 4.44e-01 2.84e+02
  angle pdb=" N   ALA B 231 "
        pdb=" CA  ALA B 231 "
        pdb=" C   ALA B 231 "
      ideal   model   delta    sigma   weight residual
     109.96   84.69   25.27 1.50e+00 4.44e-01 2.84e+02
  angle pdb=" N   ILE A 144 "
        pdb=" CA  ILE A 144 "
        pdb=" C   ILE A 144 "
      ideal   model   delta    sigma   weight residual
     111.05  129.95  -18.90 1.25e+00 6.40e-01 2.29e+02
  ... (remaining 9755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 3573
       16.24 -    32.49: 425
       32.49 -    48.73: 138
       48.73 -    64.98: 20
       64.98 -    81.22: 10
  Dihedral angle restraints: 4166
    sinusoidal: 1514
      harmonic: 2652
  Sorted by residual:
  dihedral pdb=" C   ILE B 144 "
           pdb=" N   ILE B 144 "
           pdb=" CA  ILE B 144 "
           pdb=" CB  ILE B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -157.38   35.38     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" C   ILE A 144 "
           pdb=" N   ILE A 144 "
           pdb=" CA  ILE A 144 "
           pdb=" CB  ILE A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -157.38   35.38     0      2.50e+00 1.60e-01 2.00e+02
  dihedral pdb=" N   ILE B 144 "
           pdb=" C   ILE B 144 "
           pdb=" CA  ILE B 144 "
           pdb=" CB  ILE B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  156.10  -32.70     0      2.50e+00 1.60e-01 1.71e+02
  ... (remaining 4163 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.296: 1170
       0.296 -    0.592: 2
       0.592 -    0.888: 0
       0.888 -    1.184: 2
       1.184 -    1.480: 2
  Chirality restraints: 1176
  Sorted by residual:
  chirality pdb=" CA  ILE B 144 "
            pdb=" N   ILE B 144 "
            pdb=" C   ILE B 144 "
            pdb=" CB  ILE B 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    0.95    1.48 2.00e-01 2.50e+01 5.47e+01
  chirality pdb=" CA  ILE A 144 "
            pdb=" N   ILE A 144 "
            pdb=" C   ILE A 144 "
            pdb=" CB  ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    0.95    1.48 2.00e-01 2.50e+01 5.47e+01
  chirality pdb=" CA  ALA A 145 "
            pdb=" N   ALA A 145 "
            pdb=" C   ALA A 145 "
            pdb=" CB  ALA A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.52    0.96 2.00e-01 2.50e+01 2.32e+01
  ... (remaining 1173 not shown)

  Planarity restraints: 1196
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 439 "    0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO A 440 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 440 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 440 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 439 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO B 440 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 440 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 440 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  67 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   ASP B  67 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASP B  67 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  68 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1193 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 8
        1.93 -     2.67: 145
        2.67 -     3.42: 10060
        3.42 -     4.16: 15053
        4.16 -     4.90: 28459
  Nonbonded interactions: 53725
  Sorted by model distance:
  nonbonded pdb=" CH2 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.191 3.760
  nonbonded pdb=" CE  MET A 450 "
            pdb=" CH2 TRP B 458 "
     model   vdw
     1.194 3.760
  nonbonded pdb=" CZ3 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.577 3.760
  nonbonded pdb=" CE  MET A 450 "
            pdb=" CZ3 TRP B 458 "
     model   vdw
     1.579 3.760
  nonbonded pdb=" CZ2 TRP A 458 "
            pdb=" CE  MET B 450 "
     model   vdw
     1.815 3.760
  ... (remaining 53720 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: 0.03
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.370
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
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      :  0.003   0.070   7196  Z= 0.169
  Angle     :  1.112  25.275   9768  Z= 0.685
  Chirality :  0.087   1.480   1176
  Planarity :  0.004   0.043   1196
  Dihedral  : 15.664  81.221   2474
  Min Nonbonded Distance : 1.191

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.40 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.95 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.27), residues: 936
  helix:  0.54 (0.23), residues: 534
  sheet:  None (None), residues: 0
  loop : -2.98 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 253 
 HIS   0.001   0.000   HIS B 297 
 PHE   0.014   0.001   PHE A 368 
 TYR   0.017   0.001   TYR B  98 
 ARG   0.001   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17791 (  346)
  hydrogen bonds       : angle       4.91709 ( 1002)
  SS BOND              : bond        0.00268 (    4)
  SS BOND              : angle       1.82478 (    8)
  covalent geometry    : bond        0.00348 ( 7192)
  covalent geometry    : angle       1.11142 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 MET cc_start: 0.6159 (mmt) cc_final: 0.5882 (mmt)
REVERT: B  163 MET cc_start: 0.6141 (mmt) cc_final: 0.5834 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 115
  average time/residue: 0.1402
  time to fit residues: 23.5696
Evaluate side-chains
  120 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.168744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.135204 restraints weight = 9966.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.89
r_work: 0.3468 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7196  Z= 0.150
  Angle     :  0.594   7.943   9768  Z= 0.312
  Chirality :  0.039   0.121   1176
  Planarity :  0.004   0.044   1196
  Dihedral  :  5.629  48.118   1006
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 24.19 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.28), residues: 936
  helix:  0.74 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -3.08 (0.27), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 253 
 HIS   0.002   0.001   HIS B 297 
 PHE   0.018   0.001   PHE A 468 
 TYR   0.008   0.001   TYR A 375 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04210 (  346)
  hydrogen bonds       : angle       3.68630 ( 1002)
  SS BOND              : bond        0.00425 (    4)
  SS BOND              : angle       1.63531 (    8)
  covalent geometry    : bond        0.00355 ( 7192)
  covalent geometry    : angle       0.59199 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  463 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7634 (mm-30)
REVERT: A  492 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8303 (tm)
REVERT: B  450 MET cc_start: 0.8756 (ttp) cc_final: 0.8394 (ttt)
REVERT: B  463 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7614 (mm-30)
REVERT: B  492 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8313 (tm)
  outliers start: 30
  outliers final: 14
  residues processed: 143
  average time/residue: 0.1256
  time to fit residues: 26.6407
Evaluate side-chains
  128 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.165757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132303 restraints weight = 10164.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.91
r_work: 0.3429 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7196  Z= 0.167
  Angle     :  0.584   7.587   9768  Z= 0.308
  Chirality :  0.040   0.119   1176
  Planarity :  0.004   0.045   1196
  Dihedral  :  5.655  50.148   1006
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 24.73 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.28), residues: 936
  helix:  1.07 (0.23), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.87 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 253 
 HIS   0.002   0.001   HIS A 297 
 PHE   0.014   0.001   PHE B 468 
 TYR   0.009   0.001   TYR A 375 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  346)
  hydrogen bonds       : angle       3.64007 ( 1002)
  SS BOND              : bond        0.00441 (    4)
  SS BOND              : angle       1.72543 (    8)
  covalent geometry    : bond        0.00401 ( 7192)
  covalent geometry    : angle       0.58246 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  409 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8309 (m)
REVERT: A  463 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7612 (mm-30)
REVERT: A  492 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8433 (tm)
REVERT: B  463 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7617 (mm-30)
REVERT: B  492 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8446 (tm)
  outliers start: 38
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1301
  time to fit residues: 27.7680
Evaluate side-chains
  142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 34 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.170116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.136681 restraints weight = 10178.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.94
r_work: 0.3482 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7196  Z= 0.112
  Angle     :  0.548  10.770   9768  Z= 0.285
  Chirality :  0.038   0.132   1176
  Planarity :  0.004   0.045   1196
  Dihedral  :  5.442  48.299   1006
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 26.21 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.28), residues: 936
  helix:  1.14 (0.23), residues: 562
  sheet:  None (None), residues: 0
  loop : -2.85 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS A 297 
 PHE   0.011   0.001   PHE A 468 
 TYR   0.005   0.001   TYR A 375 
 ARG   0.001   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  346)
  hydrogen bonds       : angle       3.40631 ( 1002)
  SS BOND              : bond        0.00332 (    4)
  SS BOND              : angle       1.65550 (    8)
  covalent geometry    : bond        0.00256 ( 7192)
  covalent geometry    : angle       0.54612 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8228 (tt)
REVERT: A  463 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7617 (mm-30)
REVERT: A  492 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8381 (tm)
REVERT: B  185 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: B  362 PHE cc_start: 0.7482 (m-10) cc_final: 0.7230 (m-10)
REVERT: B  463 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7623 (mm-30)
REVERT: B  492 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8382 (tm)
  outliers start: 31
  outliers final: 18
  residues processed: 141
  average time/residue: 0.1325
  time to fit residues: 27.4826
Evaluate side-chains
  140 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0470
   chunk 28 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 76 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8482

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.168864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.135567 restraints weight = 10044.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.91
r_work: 0.3466 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7196  Z= 0.125
  Angle     :  0.555   8.808   9768  Z= 0.290
  Chirality :  0.038   0.125   1176
  Planarity :  0.004   0.045   1196
  Dihedral  :  5.442  49.190   1006
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 26.48 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.28), residues: 936
  helix:  1.14 (0.23), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.98 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 297 
 PHE   0.011   0.001   PHE A 468 
 TYR   0.007   0.001   TYR A  98 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  346)
  hydrogen bonds       : angle       3.39959 ( 1002)
  SS BOND              : bond        0.00371 (    4)
  SS BOND              : angle       1.66284 (    8)
  covalent geometry    : bond        0.00293 ( 7192)
  covalent geometry    : angle       0.55335 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8334 (tt)
REVERT: A  463 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7628 (mm-30)
REVERT: A  492 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8375 (tm)
REVERT: B  185 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: B  362 PHE cc_start: 0.7496 (m-10) cc_final: 0.7237 (m-10)
REVERT: B  463 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7627 (mm-30)
REVERT: B  492 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8353 (tm)
  outliers start: 31
  outliers final: 23
  residues processed: 141
  average time/residue: 0.1320
  time to fit residues: 27.4542
Evaluate side-chains
  148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.166077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.132888 restraints weight = 10092.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.90
r_work: 0.3426 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7196  Z= 0.159
  Angle     :  0.585   7.374   9768  Z= 0.308
  Chirality :  0.040   0.121   1176
  Planarity :  0.004   0.048   1196
  Dihedral  :  5.619  51.559   1006
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 25.27 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.28), residues: 936
  helix:  1.35 (0.23), residues: 552
  sheet:  None (None), residues: 0
  loop : -2.82 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B 297 
 PHE   0.010   0.001   PHE B 368 
 TYR   0.008   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  346)
  hydrogen bonds       : angle       3.56163 ( 1002)
  SS BOND              : bond        0.00419 (    4)
  SS BOND              : angle       1.79424 (    8)
  covalent geometry    : bond        0.00379 ( 7192)
  covalent geometry    : angle       0.58266 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: A  463 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7560 (mm-30)
REVERT: A  492 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8461 (tm)
REVERT: B  185 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8355 (tt)
REVERT: B  463 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7550 (mm-30)
REVERT: B  492 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8450 (tm)
  outliers start: 39
  outliers final: 29
  residues processed: 141
  average time/residue: 0.1413
  time to fit residues: 29.9174
Evaluate side-chains
  146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 6 optimal weight:    0.0970
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.171133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137676 restraints weight = 9877.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.92
r_work: 0.3492 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7196  Z= 0.107
  Angle     :  0.535   7.951   9768  Z= 0.281
  Chirality :  0.038   0.133   1176
  Planarity :  0.004   0.049   1196
  Dihedral  :  5.344  49.640   1006
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.40 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.28), residues: 936
  helix:  1.33 (0.23), residues: 560
  sheet:  None (None), residues: 0
  loop : -2.79 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 253 
 HIS   0.002   0.000   HIS A 160 
 PHE   0.011   0.001   PHE A 368 
 TYR   0.007   0.001   TYR B  98 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03174 (  346)
  hydrogen bonds       : angle       3.32107 ( 1002)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       1.73487 (    8)
  covalent geometry    : bond        0.00244 ( 7192)
  covalent geometry    : angle       0.53322 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: A  463 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7578 (mm-30)
REVERT: B  185 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: B  362 PHE cc_start: 0.7518 (m-10) cc_final: 0.7260 (m-10)
REVERT: B  463 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7584 (mm-30)
REVERT: B  492 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (tm)
  outliers start: 36
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1401
  time to fit residues: 30.1749
Evaluate side-chains
  143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  492 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.136836 restraints weight = 10005.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.91
r_work: 0.3481 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7196  Z= 0.120
  Angle     :  0.556   8.536   9768  Z= 0.292
  Chirality :  0.039   0.141   1176
  Planarity :  0.004   0.051   1196
  Dihedral  :  5.361  50.910   1006
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 25.13 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.28), residues: 936
  helix:  1.28 (0.23), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.90 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.010   0.001   PHE B 368 
 TYR   0.008   0.001   TYR B  98 
 ARG   0.001   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  346)
  hydrogen bonds       : angle       3.34315 ( 1002)
  SS BOND              : bond        0.00358 (    4)
  SS BOND              : angle       1.71233 (    8)
  covalent geometry    : bond        0.00278 ( 7192)
  covalent geometry    : angle       0.55375 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8319 (tt)
REVERT: A  317 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7686 (mt)
REVERT: A  463 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7582 (mm-30)
REVERT: B  185 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: B  362 PHE cc_start: 0.7493 (m-10) cc_final: 0.7278 (m-10)
REVERT: B  463 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7620 (mm-30)
  outliers start: 37
  outliers final: 29
  residues processed: 140
  average time/residue: 0.1306
  time to fit residues: 27.1327
Evaluate side-chains
  148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    0.0370
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 74 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 160 HIS
B 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.172795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.139177 restraints weight = 10089.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.95
r_work: 0.3586 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7196  Z= 0.105
  Angle     :  0.539   9.047   9768  Z= 0.282
  Chirality :  0.038   0.128   1176
  Planarity :  0.004   0.051   1196
  Dihedral  :  5.274  50.144   1006
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 26.34 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.28), residues: 936
  helix:  1.28 (0.23), residues: 566
  sheet:  None (None), residues: 0
  loop : -2.87 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 160 
 PHE   0.013   0.001   PHE B 368 
 TYR   0.008   0.001   TYR A  98 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03030 (  346)
  hydrogen bonds       : angle       3.24942 ( 1002)
  SS BOND              : bond        0.00375 (    4)
  SS BOND              : angle       1.81727 (    8)
  covalent geometry    : bond        0.00237 ( 7192)
  covalent geometry    : angle       0.53637 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  144 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8400 (mt)
REVERT: A  185 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8261 (tt)
REVERT: A  317 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7742 (mt)
REVERT: A  463 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7504 (mm-30)
REVERT: B   99 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8201 (mm-30)
REVERT: B  185 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8270 (tt)
REVERT: B  362 PHE cc_start: 0.7491 (m-10) cc_final: 0.7259 (m-10)
REVERT: B  463 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7546 (mm-30)
  outliers start: 31
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1333
  time to fit residues: 28.7402
Evaluate side-chains
  149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  189 ILE
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 8 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0970
   chunk 90 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 68 optimal weight:    0.2980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.171648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.141372 restraints weight = 9866.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.73
r_work: 0.3612 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7196  Z= 0.105
  Angle     :  0.554   9.957   9768  Z= 0.290
  Chirality :  0.038   0.128   1176
  Planarity :  0.004   0.052   1196
  Dihedral  :  5.188  49.775   1006
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.19 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 27.28 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.28), residues: 936
  helix:  1.34 (0.23), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.81 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.014   0.001   PHE A 362 
 TYR   0.009   0.001   TYR A  98 
 ARG   0.001   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03015 (  346)
  hydrogen bonds       : angle       3.22008 ( 1002)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       1.72045 (    8)
  covalent geometry    : bond        0.00238 ( 7192)
  covalent geometry    : angle       0.55181 ( 9760)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  185 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8192 (tt)
REVERT: A  276 TYR cc_start: 0.8627 (m-10) cc_final: 0.8291 (m-10)
REVERT: A  463 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7552 (mm-30)
REVERT: B  185 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8184 (tt)
REVERT: B  276 TYR cc_start: 0.8620 (m-10) cc_final: 0.8289 (m-10)
REVERT: B  362 PHE cc_start: 0.7435 (m-10) cc_final: 0.7216 (m-10)
REVERT: B  463 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7560 (mm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 138
  average time/residue: 0.1288
  time to fit residues: 26.4202
Evaluate side-chains
  147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  232 CYS
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  419 TYR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  232 CYS
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  398 GLU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  419 TYR
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0020
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0870
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5166

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 147 ASN
B 160 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.171729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.141492 restraints weight = 9727.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.71
r_work: 0.3543 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7196  Z= 0.107
  Angle     :  0.549   9.563   9768  Z= 0.287
  Chirality :  0.038   0.132   1176
  Planarity :  0.004   0.052   1196
  Dihedral  :  5.168  49.786   1006
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 27.02 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 936
  helix:  1.31 (0.23), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.87 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.013   0.001   PHE A 362 
 TYR   0.009   0.001   TYR A  98 
 ARG   0.001   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  346)
  hydrogen bonds       : angle       3.21106 ( 1002)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       1.52760 (    8)
  covalent geometry    : bond        0.00246 ( 7192)
  covalent geometry    : angle       0.54768 ( 9760)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.98 seconds
wall clock time: 50 minutes 12.89 seconds (3012.89 seconds total)