Starting phenix.real_space_refine
on Wed Mar 12 14:46:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw5_38731/03_2025/8xw5_38731.cif"
  }
  resolution = 3.56
  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=   0.002 sd=   0.036
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      30      5.16       5
     C    5280      2.51       5
     N    1282      2.21       5
     O    1460      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8052
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4026
          Classifications: {'peptide': 543}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 524}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.32, per 1000 atoms: 0.91
  Number of scatterers: 8052
  At special positions: 0
  Unit cell: (101.652, 73.284, 112.684, 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      30     16.00
     O    1460      8.00
     N    1282      7.00
     C    5280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS B  60 " 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: 2.05
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      70.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
    Processing helix  chain 'A' and resid 11 through 19
      removed outlier: 3.546A  pdb=" N   THR A  15 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.532A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 51
      removed outlier: 3.761A  pdb=" N   LEU A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 77
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.521A  pdb=" N   LYS A  87 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 114
      removed outlier: 3.638A  pdb=" N   LEU A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A  98 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 132 through 145
      removed outlier: 4.103A  pdb=" N   GLY A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 168
      Proline residue:  A 160  - end of helix
      removed outlier: 3.990A  pdb=" N   VAL A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 180
      removed outlier: 3.566A  pdb=" N   ILE A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 186
      removed outlier: 3.647A  pdb=" N   LYS A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 201
      removed outlier: 3.500A  pdb=" N   LEU A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 236
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 3.570A  pdb=" N   LEU A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLN A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 4.047A  pdb=" N   THR A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 353
      removed outlier: 3.648A  pdb=" N   GLU A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 381
      removed outlier: 3.762A  pdb=" N   VAL A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 412
      removed outlier: 3.809A  pdb=" N   THR A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 442
      removed outlier: 4.008A  pdb=" N   LEU A 431 " --> pdb=" O   GLN A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 3.696A  pdb=" N   GLN A 451 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 479
      Proline residue:  A 468  - end of helix
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.896A  pdb=" N   LEU A 501 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ASN A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 503 " --> pdb=" O   ALA A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 543
      Proline residue:  A 522  - end of helix
      removed outlier: 3.662A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      Proline residue:  A 536  - end of helix
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 3.546A  pdb=" N   THR B  15 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 3.532A  pdb=" N   LEU B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 51
      removed outlier: 3.761A  pdb=" N   LEU B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU B  48 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 77
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.521A  pdb=" N   LYS B  87 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 114
      removed outlier: 3.638A  pdb=" N   LEU B  97 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B  98 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 132 through 145
      removed outlier: 4.103A  pdb=" N   GLY B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 168
      Proline residue:  B 160  - end of helix
      removed outlier: 3.991A  pdb=" N   VAL B 168 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 180
      removed outlier: 3.566A  pdb=" N   ILE B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B 175 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 186
      removed outlier: 3.647A  pdb=" N   LYS B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 201
      removed outlier: 3.500A  pdb=" N   LEU B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 266 through 278
    Processing helix  chain 'B' and resid 301 through 312
      removed outlier: 3.570A  pdb=" N   LEU B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLN B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASP B 310 " --> pdb=" O   LYS B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 331
      removed outlier: 4.047A  pdb=" N   THR B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 353
      removed outlier: 3.648A  pdb=" N   GLU B 348 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 381
      removed outlier: 3.762A  pdb=" N   VAL B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 412
      removed outlier: 3.808A  pdb=" N   THR B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 442
      removed outlier: 4.008A  pdb=" N   LEU B 431 " --> pdb=" O   GLN B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 452
      removed outlier: 3.696A  pdb=" N   GLN B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 479
      Proline residue:  B 468  - end of helix
    Processing helix  chain 'B' and resid 483 through 496
    Processing helix  chain 'B' and resid 497 through 509
      removed outlier: 3.896A  pdb=" N   LEU B 501 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASN B 502 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B 503 " --> pdb=" O   ALA B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 543
      Proline residue:  B 522  - end of helix
      removed outlier: 3.662A  pdb=" N   ILE B 526 " --> pdb=" O   PRO B 522 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      Proline residue:  B 536  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 245
      removed outlier: 6.449A  pdb=" N   ALA A 262 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU A 245 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL A 260 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR A 216 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A 280 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 385
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 245
      removed outlier: 6.449A  pdb=" N   ALA B 262 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU B 245 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL B 260 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR B 216 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU B 280 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 316
    Processing sheet with id=AA8, first strand: chain 'B' and resid 382 through 385

    527 hydrogen bonds defined for protein.
    1563 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2504
        1.34 -     1.46: 1307
        1.46 -     1.57: 4329
        1.57 -     1.69: 0
        1.69 -     1.80: 58
  Bond restraints: 8198
  Sorted by residual:
  bond pdb=" N   VAL A 208 "
       pdb=" CA  VAL A 208 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   VAL B 208 "
       pdb=" CA  VAL B 208 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.22e-02 6.72e+03 8.79e+00
  bond pdb=" N   ILE A 204 "
       pdb=" CA  ILE A 204 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.23e-02 6.61e+03 7.40e+00
  bond pdb=" N   ILE B 204 "
       pdb=" CA  ILE B 204 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.033 1.23e-02 6.61e+03 7.40e+00
  bond pdb=" N   VAL A 206 "
       pdb=" CA  VAL A 206 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.23e-02 6.61e+03 7.14e+00
  ... (remaining 8193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 10714
        1.13 -     2.25: 316
        2.25 -     3.38: 68
        3.38 -     4.51: 26
        4.51 -     5.63: 12
  Bond angle restraints: 11136
  Sorted by residual:
  angle pdb=" CB  GLU B 281 "
        pdb=" CG  GLU B 281 "
        pdb=" CD  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     112.60  117.52   -4.92 1.70e+00 3.46e-01 8.38e+00
  angle pdb=" CB  GLU A 281 "
        pdb=" CG  GLU A 281 "
        pdb=" CD  GLU A 281 "
      ideal   model   delta    sigma   weight residual
     112.60  117.52   -4.92 1.70e+00 3.46e-01 8.38e+00
  angle pdb=" CA  GLU B 281 "
        pdb=" CB  GLU B 281 "
        pdb=" CG  GLU B 281 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.93e+00
  angle pdb=" CA  GLU A 281 "
        pdb=" CB  GLU A 281 "
        pdb=" CG  GLU A 281 "
      ideal   model   delta    sigma   weight residual
     114.10  119.70   -5.60 2.00e+00 2.50e-01 7.85e+00
  angle pdb=" CA  VAL B 208 "
        pdb=" C   VAL B 208 "
        pdb=" O   VAL B 208 "
      ideal   model   delta    sigma   weight residual
     121.40  118.32    3.08 1.27e+00 6.20e-01 5.87e+00
  ... (remaining 11131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 4208
       14.85 -    29.71: 448
       29.71 -    44.56: 132
       44.56 -    59.42: 27
       59.42 -    74.27: 20
  Dihedral angle restraints: 4835
    sinusoidal: 1759
      harmonic: 3076
  Sorted by residual:
  dihedral pdb=" CB  CYS A  60 "
           pdb=" SG  CYS A  60 "
           pdb=" SG  CYS B  60 "
           pdb=" CB  CYS B  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.25   42.25     1      1.00e+01 1.00e-02 2.49e+01
  dihedral pdb=" CA  ASN A 432 "
           pdb=" CB  ASN A 432 "
           pdb=" CG  ASN A 432 "
           pdb=" OD1 ASN A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.73  -74.27     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ASN B 432 "
           pdb=" CB  ASN B 432 "
           pdb=" CG  ASN B 432 "
           pdb=" OD1 ASN B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.73  -74.27     2      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 4832 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1005
       0.040 -    0.080: 281
       0.080 -    0.120: 82
       0.120 -    0.160: 10
       0.160 -    0.200: 4
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" CA  VAL A 208 "
            pdb=" N   VAL A 208 "
            pdb=" C   VAL A 208 "
            pdb=" CB  VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.92e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 281 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" CD  GLU A 281 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 281 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 281 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 281 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" CD  GLU B 281 "   -0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 281 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 281 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 324 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 325 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1837
        2.78 -     3.31: 8087
        3.31 -     3.84: 13658
        3.84 -     4.37: 14975
        4.37 -     4.90: 26881
  Nonbonded interactions: 65438
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 140 "
            pdb=" OG  SER B 143 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLU A 140 "
            pdb=" OG  SER A 143 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE1 GLN A 227 "
            pdb=" NZ  LYS A 235 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" OE1 GLN B 227 "
            pdb=" NZ  LYS B 235 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" NH1 ARG A 179 "
            pdb=" OD2 ASP A 503 "
     model   vdw
     2.394 3.120
  ... (remaining 65433 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.530
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:3.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
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   0.039   8198  Z= 0.194
  Angle     :  0.526   5.632  11136  Z= 0.296
  Chirality :  0.041   0.200   1382
  Planarity :  0.004   0.030   1378
  Dihedral  : 14.483  74.272   2868
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 16.98 %
    Favored  : 82.79 %
  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:  0.96 (0.26), residues: 1082
  helix:  1.07 (0.19), residues: 736
  sheet: -0.40 (0.77), residues: 56
  loop : -0.03 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 367 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.013   0.001   PHE B 111 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 179 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  112 LYS cc_start: 0.7096 (tttt) cc_final: 0.6679 (tppt)
REVERT: A  227 GLN cc_start: 0.6908 (mt0) cc_final: 0.6407 (mm-40)
REVERT: B  227 GLN cc_start: 0.6555 (mt0) cc_final: 0.6300 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1948
  time to fit residues: 22.4117
Evaluate side-chains
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  51 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.184482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150646 restraints weight = 8557.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.155081 restraints weight = 5435.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.157949 restraints weight = 4113.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8198  Z= 0.236
  Angle     :  0.511   6.408  11136  Z= 0.273
  Chirality :  0.041   0.130   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.640  59.370   1130
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 13.84 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.00 (0.25), residues: 1082
  helix:  1.11 (0.19), residues: 740
  sheet: -0.53 (0.79), residues: 56
  loop : -0.02 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 367 
 HIS   0.004   0.001   HIS B 414 
 PHE   0.010   0.001   PHE A  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.002   0.001   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7896 (tt)
REVERT: A  112 LYS cc_start: 0.7872 (tttt) cc_final: 0.7581 (tppt)
REVERT: A  203 MET cc_start: 0.7511 (mtt) cc_final: 0.7158 (mtp)
REVERT: A  256 ASN cc_start: 0.6823 (p0) cc_final: 0.6579 (p0)
REVERT: A  281 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: B   20 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8158 (tt)
REVERT: B   85 MET cc_start: 0.8038 (mmp) cc_final: 0.7786 (mmt)
REVERT: B  186 MET cc_start: 0.7290 (mtm) cc_final: 0.7088 (mtp)
  outliers start: 38
  outliers final: 24
  residues processed: 109
  average time/residue: 0.1708
  time to fit residues: 27.4534
Evaluate side-chains
  100 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  492 THR
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 105 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0050
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 227 GLN
B 469 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.197303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.165454 restraints weight = 8772.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.169088 restraints weight = 6183.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.171478 restraints weight = 4955.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8198  Z= 0.191
  Angle     :  0.465   5.912  11136  Z= 0.250
  Chirality :  0.039   0.129   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.570  58.953   1130
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.65 %
    Favored  : 82.09 %
  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:  1.18 (0.25), residues: 1082
  helix:  1.25 (0.19), residues: 740
  sheet: -0.18 (0.86), residues: 52
  loop : -0.06 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE A 515 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8034 (tt)
REVERT: A  112 LYS cc_start: 0.7951 (tttt) cc_final: 0.7683 (tppt)
REVERT: A  182 MET cc_start: 0.7740 (ttt) cc_final: 0.7505 (ttt)
REVERT: A  203 MET cc_start: 0.7564 (mtt) cc_final: 0.7242 (mtp)
REVERT: A  299 ASN cc_start: 0.7382 (m-40) cc_final: 0.7143 (p0)
REVERT: A  321 ASP cc_start: 0.7541 (p0) cc_final: 0.7306 (p0)
REVERT: A  433 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8227 (tp)
REVERT: B   20 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8134 (tt)
REVERT: B  182 MET cc_start: 0.8404 (tpp) cc_final: 0.8094 (ttt)
REVERT: B  186 MET cc_start: 0.7242 (mtm) cc_final: 0.6918 (mtp)
REVERT: B  433 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8138 (tt)
  outliers start: 28
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1730
  time to fit residues: 28.8753
Evaluate side-chains
  105 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.223014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.194043 restraints weight = 8647.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.196562 restraints weight = 6621.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.198289 restraints weight = 5557.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8198  Z= 0.232
  Angle     :  0.497   6.238  11136  Z= 0.265
  Chirality :  0.041   0.129   1382
  Planarity :  0.004   0.037   1378
  Dihedral  :  4.605  59.827   1130
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.70 %
    Favored  : 80.58 %
  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:  1.18 (0.26), residues: 1082
  helix:  1.23 (0.19), residues: 728
  sheet: -0.36 (0.77), residues: 62
  loop :  0.13 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE A 515 
 TYR   0.016   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8056 (tt)
REVERT: A  182 MET cc_start: 0.7632 (ttt) cc_final: 0.7406 (ttt)
REVERT: A  321 ASP cc_start: 0.7480 (p0) cc_final: 0.7264 (p0)
REVERT: A  433 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8294 (tp)
REVERT: B   20 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7951 (tt)
REVERT: B  182 MET cc_start: 0.8393 (tpp) cc_final: 0.8133 (ttt)
REVERT: B  433 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (tp)
  outliers start: 32
  outliers final: 25
  residues processed: 112
  average time/residue: 0.1667
  time to fit residues: 27.4691
Evaluate side-chains
  107 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4123 r_free = 0.4123 target = 0.186717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.152329 restraints weight = 8656.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.156820 restraints weight = 5631.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.159587 restraints weight = 4304.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8198  Z= 0.184
  Angle     :  0.476   6.242  11136  Z= 0.251
  Chirality :  0.040   0.127   1382
  Planarity :  0.004   0.035   1378
  Dihedral  :  4.548  57.976   1130
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 16.05 %
    Favored  : 79.65 %
  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:  1.21 (0.26), residues: 1082
  helix:  1.35 (0.19), residues: 740
  sheet: -0.38 (0.78), residues: 62
  loop : -0.22 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B  76 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 77
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7926 (tt)
REVERT: A  182 MET cc_start: 0.7671 (ttt) cc_final: 0.7432 (ttt)
REVERT: A  235 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7545 (ttpp)
REVERT: A  321 ASP cc_start: 0.7426 (p0) cc_final: 0.7211 (p0)
REVERT: A  433 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8177 (tp)
REVERT: B   20 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7919 (tt)
REVERT: B  186 MET cc_start: 0.7187 (mtm) cc_final: 0.6860 (mtp)
REVERT: B  433 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8104 (tt)
  outliers start: 37
  outliers final: 24
  residues processed: 103
  average time/residue: 0.1597
  time to fit residues: 24.3720
Evaluate side-chains
  101 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 107 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0060
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.186443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151510 restraints weight = 8671.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156003 restraints weight = 5606.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158890 restraints weight = 4295.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8198  Z= 0.193
  Angle     :  0.483   6.277  11136  Z= 0.256
  Chirality :  0.040   0.149   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.510  57.518   1130
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.28 %
    Favored  : 80.23 %
  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:  1.24 (0.26), residues: 1082
  helix:  1.39 (0.19), residues: 740
  sheet: -0.71 (0.86), residues: 56
  loop : -0.16 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.014   0.001   TYR A 216 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.7971 (tt)
REVERT: A  182 MET cc_start: 0.7751 (ttt) cc_final: 0.7476 (ttt)
REVERT: A  235 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7925 (ptpp)
REVERT: A  321 ASP cc_start: 0.7431 (p0) cc_final: 0.7199 (p0)
REVERT: A  433 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8163 (tp)
REVERT: B   20 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7951 (tt)
REVERT: B  433 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8108 (tt)
  outliers start: 30
  outliers final: 22
  residues processed: 92
  average time/residue: 0.1787
  time to fit residues: 23.6153
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 101 optimal weight:    0.2980
   chunk 102 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4133 r_free = 0.4133 target = 0.187647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154456 restraints weight = 8726.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.156304 restraints weight = 6276.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.158994 restraints weight = 4799.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8198  Z= 0.176
  Angle     :  0.471   5.800  11136  Z= 0.248
  Chirality :  0.040   0.135   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.462  57.191   1130
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.86 %
    Favored  : 79.77 %
  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:  1.33 (0.26), residues: 1082
  helix:  1.47 (0.19), residues: 742
  sheet: -0.75 (0.85), residues: 56
  loop : -0.17 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 367 
 HIS   0.002   0.000   HIS A 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.014   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 355 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7919 (tt)
REVERT: A  235 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7927 (ptpp)
REVERT: A  321 ASP cc_start: 0.7427 (p0) cc_final: 0.7196 (p0)
REVERT: A  433 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8177 (tp)
REVERT: B   20 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7877 (tt)
REVERT: B  112 LYS cc_start: 0.7849 (tttt) cc_final: 0.7548 (tppt)
REVERT: B  433 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (tt)
  outliers start: 29
  outliers final: 20
  residues processed: 95
  average time/residue: 0.1947
  time to fit residues: 25.9542
Evaluate side-chains
  96 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.186437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153187 restraints weight = 8808.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155570 restraints weight = 6034.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.158426 restraints weight = 4636.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8198  Z= 0.200
  Angle     :  0.484   6.204  11136  Z= 0.256
  Chirality :  0.040   0.174   1382
  Planarity :  0.003   0.034   1378
  Dihedral  :  4.476  57.686   1130
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.21 %
    Favored  : 79.30 %
  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:  1.28 (0.26), residues: 1082
  helix:  1.43 (0.19), residues: 740
  sheet: -0.70 (0.86), residues: 56
  loop : -0.20 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7967 (tt)
REVERT: A  186 MET cc_start: 0.6984 (ttp) cc_final: 0.6731 (mtp)
REVERT: A  235 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7964 (ptpp)
REVERT: A  321 ASP cc_start: 0.7436 (p0) cc_final: 0.7211 (p0)
REVERT: A  433 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8173 (tp)
REVERT: B   20 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7860 (tt)
REVERT: B  112 LYS cc_start: 0.7872 (tttt) cc_final: 0.7567 (tppt)
REVERT: B  281 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8302 (tm-30)
REVERT: B  433 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8116 (tp)
  outliers start: 30
  outliers final: 22
  residues processed: 103
  average time/residue: 0.1836
  time to fit residues: 26.9654
Evaluate side-chains
  106 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.151332 restraints weight = 8846.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.155653 restraints weight = 5803.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.158486 restraints weight = 4459.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8198  Z= 0.208
  Angle     :  0.491   6.316  11136  Z= 0.259
  Chirality :  0.040   0.142   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.496  57.648   1130
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.67 %
    Favored  : 78.95 %
  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:  1.24 (0.26), residues: 1082
  helix:  1.42 (0.19), residues: 740
  sheet: -0.75 (0.76), residues: 66
  loop : -0.25 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 367 
 HIS   0.004   0.001   HIS B 187 
 PHE   0.010   0.001   PHE B  69 
 TYR   0.016   0.001   TYR B 216 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8001 (tt)
REVERT: A  321 ASP cc_start: 0.7439 (p0) cc_final: 0.7204 (p0)
REVERT: A  433 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8197 (tp)
REVERT: B   20 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7979 (tt)
REVERT: B  112 LYS cc_start: 0.7878 (tttt) cc_final: 0.7591 (tppt)
REVERT: B  281 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: B  433 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8159 (tp)
  outliers start: 29
  outliers final: 22
  residues processed: 108
  average time/residue: 0.1632
  time to fit residues: 26.0385
Evaluate side-chains
  113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.197339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164367 restraints weight = 8767.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.168121 restraints weight = 6074.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.170538 restraints weight = 4829.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8198  Z= 0.182
  Angle     :  0.480   6.074  11136  Z= 0.252
  Chirality :  0.040   0.187   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.448  57.055   1130
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.26 %
    Favored  : 78.60 %
  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:  1.38 (0.26), residues: 1082
  helix:  1.53 (0.19), residues: 742
  sheet: -0.76 (0.77), residues: 66
  loop : -0.19 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 367 
 HIS   0.003   0.000   HIS B 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 355 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8010 (tt)
REVERT: A  182 MET cc_start: 0.8229 (tpp) cc_final: 0.7851 (ttt)
REVERT: A  186 MET cc_start: 0.6928 (ttp) cc_final: 0.6621 (mtp)
REVERT: A  235 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8066 (ptpp)
REVERT: A  321 ASP cc_start: 0.7457 (p0) cc_final: 0.7242 (p0)
REVERT: A  433 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (tp)
REVERT: B   20 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.7997 (tt)
REVERT: B  112 LYS cc_start: 0.7919 (tttt) cc_final: 0.7681 (tppt)
REVERT: B  433 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8191 (tt)
  outliers start: 27
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1785
  time to fit residues: 24.0926
Evaluate side-chains
  100 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.185524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150910 restraints weight = 8694.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155205 restraints weight = 5670.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157973 restraints weight = 4333.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8198  Z= 0.188
  Angle     :  0.492   6.122  11136  Z= 0.259
  Chirality :  0.040   0.206   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.445  57.154   1130
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.14 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.39 (0.26), residues: 1082
  helix:  1.53 (0.19), residues: 742
  sheet: -0.75 (0.87), residues: 56
  loop : -0.19 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 367 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.001   0.000   ARG B 355 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2353.40 seconds
wall clock time: 41 minutes 41.30 seconds (2501.30 seconds total)