Starting phenix.real_space_refine
on Wed Sep 17 10:15:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw5_38731/09_2025/8xw5_38731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw5_38731/09_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_38731/09_2025/8xw5_38731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw5_38731/09_2025/8xw5_38731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw5_38731/09_2025/8xw5_38731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw5_38731/09_2025/8xw5_38731.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.90, per 1000 atoms: 0.36
  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: 0.72
  Conformation dependent library (CDL) restraints added in 449.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.29
  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: 1.46

  Time building geometry restraints manager: 0.96 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: 0.02
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:             1.340
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.350
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.300
-------------------------------------------------------------------------------
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   8199  Z= 0.166
  Angle     :  0.526   5.632  11138  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (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
 ARG   0.002   0.000   ARG A 179 
 TYR   0.011   0.001   TYR A 216 
 PHE   0.013   0.001   PHE B 111 
 TRP   0.006   0.001   TRP B 367 
 HIS   0.002   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8198)
  covalent geometry    : angle       0.52606 (11136)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       0.70342 (    2)
  hydrogen bonds       : bond        0.09111 (  527)
  hydrogen bonds       : angle       5.04985 ( 1563)

*********************** 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  : 0.283 
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: 0.0867
  time to fit residues: 9.9149
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.5602

-------------------------------------------------------------------------------
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 = 0.4158 r_free = 0.4158 target = 0.191105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156794 restraints weight = 8646.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161676 restraints weight = 5318.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164784 restraints weight = 3952.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.166531 restraints weight = 3272.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.168071 restraints weight = 2901.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.0721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8199  Z= 0.115
  Angle     :  0.463   5.411  11138  Z= 0.248
  Chirality :  0.039   0.133   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.520  58.355   1130
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.26), residues: 1082
  helix:  1.36 (0.19), residues: 740
  sheet: -0.47 (0.77), residues: 56
  loop :  0.11 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.009   0.001   TYR A 216 
 PHE   0.009   0.001   PHE A 111 
 TRP   0.007   0.001   TRP B 367 
 HIS   0.002   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8198)
  covalent geometry    : angle       0.46255 (11136)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       0.59310 (    2)
  hydrogen bonds       : bond        0.03700 (  527)
  hydrogen bonds       : angle       4.32554 ( 1563)

*********************** 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
  93 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7714 (tt)
REVERT: A  112 LYS cc_start: 0.7850 (tttt) cc_final: 0.7590 (tppt)
REVERT: A  182 MET cc_start: 0.8229 (tpp) cc_final: 0.8024 (ttt)
REVERT: B  186 MET cc_start: 0.7253 (mtm) cc_final: 0.7045 (mtp)
  outliers start: 23
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0711
  time to fit residues: 9.0112
Evaluate side-chains
  73 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  164 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   64 ILE
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  539 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    0.0060
   chunk 105 optimal weight:    0.9990
   chunk 86 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.189805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.156309 restraints weight = 8536.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160941 restraints weight = 5377.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.163622 restraints weight = 4027.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.165894 restraints weight = 3355.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.167010 restraints weight = 2948.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8199  Z= 0.112
  Angle     :  0.445   5.399  11138  Z= 0.239
  Chirality :  0.039   0.128   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.478  59.083   1130
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.30 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1082
  helix:  1.47 (0.19), residues: 740
  sheet: -0.02 (0.86), residues: 52
  loop :  0.09 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  76 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.007   0.001   TRP B 367 
 HIS   0.003   0.000   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8198)
  covalent geometry    : angle       0.44483 (11136)
  SS BOND              : bond        0.00376 (    1)
  SS BOND              : angle       0.74022 (    2)
  hydrogen bonds       : bond        0.03614 (  527)
  hydrogen bonds       : angle       4.15719 ( 1563)

*********************** 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
  105 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7856 (tt)
REVERT: A  112 LYS cc_start: 0.7876 (tttt) cc_final: 0.7568 (tppt)
REVERT: A  182 MET cc_start: 0.8270 (tpp) cc_final: 0.7814 (ttt)
REVERT: A  203 MET cc_start: 0.7437 (mtt) cc_final: 0.7128 (mtp)
REVERT: A  433 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (tp)
REVERT: B  182 MET cc_start: 0.8269 (tpp) cc_final: 0.8028 (ttt)
REVERT: B  186 MET cc_start: 0.7209 (mtm) cc_final: 0.6903 (mtp)
REVERT: B  433 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7979 (tt)
  outliers start: 29
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0781
  time to fit residues: 10.7314
Evaluate side-chains
  90 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  539 ILE
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  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  433 LEU
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 45 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.7184

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.181253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.147074 restraints weight = 8873.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.151192 restraints weight = 5762.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153711 restraints weight = 4427.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155734 restraints weight = 3739.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.156764 restraints weight = 3331.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8199  Z= 0.178
  Angle     :  0.533   6.780  11138  Z= 0.284
  Chirality :  0.042   0.155   1382
  Planarity :  0.004   0.035   1378
  Dihedral  :  4.681  61.092   1130
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.12 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.25), residues: 1082
  helix:  1.16 (0.19), residues: 736
  sheet: -0.17 (0.88), residues: 52
  loop : -0.27 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 409 
 TYR   0.019   0.002   TYR B 216 
 PHE   0.012   0.002   PHE A  69 
 TRP   0.005   0.002   TRP B 367 
 HIS   0.005   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8198)
  covalent geometry    : angle       0.53329 (11136)
  SS BOND              : bond        0.00282 (    1)
  SS BOND              : angle       0.30273 (    2)
  hydrogen bonds       : bond        0.04557 (  527)
  hydrogen bonds       : angle       4.43615 ( 1563)

*********************** 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
  139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8085 (tt)
REVERT: A  112 LYS cc_start: 0.7969 (tttt) cc_final: 0.7643 (tppt)
REVERT: A  182 MET cc_start: 0.8252 (tpp) cc_final: 0.7809 (ttt)
REVERT: A  235 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7732 (ttpp)
REVERT: A  321 ASP cc_start: 0.7525 (p0) cc_final: 0.7268 (p0)
REVERT: A  433 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8212 (tp)
REVERT: B  182 MET cc_start: 0.8457 (tpp) cc_final: 0.8177 (ttt)
  outliers start: 35
  outliers final: 25
  residues processed: 129
  average time/residue: 0.0703
  time to fit residues: 13.3476
Evaluate side-chains
  117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  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  445 THR
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   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  415 MET
Chi-restraints excluded: chain B residue  445 THR
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 3 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.197592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.166561 restraints weight = 8757.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.168243 restraints weight = 7165.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.170454 restraints weight = 5630.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.171254 restraints weight = 4286.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.171278 restraints weight = 4123.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8199  Z= 0.122
  Angle     :  0.474   6.438  11138  Z= 0.249
  Chirality :  0.039   0.128   1382
  Planarity :  0.003   0.036   1378
  Dihedral  :  4.556  57.994   1130
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.26), residues: 1082
  helix:  1.39 (0.19), residues: 744
  sheet: -0.24 (0.77), residues: 62
  loop : -0.17 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 409 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8198)
  covalent geometry    : angle       0.47401 (11136)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.33492 (    2)
  hydrogen bonds       : bond        0.03802 (  527)
  hydrogen bonds       : angle       4.20085 ( 1563)

*********************** 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
  103 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7885 (tt)
REVERT: A  112 LYS cc_start: 0.7947 (tttt) cc_final: 0.7716 (tppt)
REVERT: A  182 MET cc_start: 0.8205 (tpp) cc_final: 0.7870 (ttt)
REVERT: A  321 ASP cc_start: 0.7431 (p0) cc_final: 0.7221 (p0)
REVERT: A  433 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (tt)
  outliers start: 31
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0679
  time to fit residues: 10.0860
Evaluate side-chains
  88 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   29 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  282 VAL
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   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  282 VAL
Chi-restraints excluded: chain B residue  380 ILE
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 11 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.196332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.165201 restraints weight = 8697.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.167721 restraints weight = 7189.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.169393 restraints weight = 5636.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169665 restraints weight = 4299.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.169859 restraints weight = 4150.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8199  Z= 0.135
  Angle     :  0.494   7.816  11138  Z= 0.259
  Chirality :  0.040   0.144   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.525  57.967   1130
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.26), residues: 1082
  helix:  1.44 (0.19), residues: 736
  sheet: -0.20 (0.78), residues: 62
  loop : -0.24 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.015   0.001   TYR B 216 
 PHE   0.011   0.001   PHE A  69 
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8198)
  covalent geometry    : angle       0.49413 (11136)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.37319 (    2)
  hydrogen bonds       : bond        0.03909 (  527)
  hydrogen bonds       : angle       4.20940 ( 1563)

*********************** 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
  98 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7914 (tt)
REVERT: A  112 LYS cc_start: 0.7963 (tttt) cc_final: 0.7700 (tppt)
REVERT: A  182 MET cc_start: 0.8262 (tpp) cc_final: 0.7864 (ttt)
REVERT: A  227 GLN cc_start: 0.7991 (mt0) cc_final: 0.7454 (mm-40)
REVERT: A  321 ASP cc_start: 0.7413 (p0) cc_final: 0.7190 (p0)
REVERT: A  433 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8247 (tt)
  outliers start: 25
  outliers final: 21
  residues processed: 91
  average time/residue: 0.0756
  time to fit residues: 10.1933
Evaluate side-chains
  95 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   29 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  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   29 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  380 ILE
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 48 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.194547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.162861 restraints weight = 8748.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.165008 restraints weight = 7272.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.167015 restraints weight = 5657.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.167542 restraints weight = 4348.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.167615 restraints weight = 4203.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8199  Z= 0.148
  Angle     :  0.508   7.555  11138  Z= 0.267
  Chirality :  0.041   0.139   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.563  58.359   1130
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.40 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1082
  helix:  1.35 (0.19), residues: 736
  sheet: -0.65 (0.76), residues: 66
  loop : -0.25 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.017   0.001   TYR B 216 
 PHE   0.011   0.001   PHE A  69 
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8198)
  covalent geometry    : angle       0.50777 (11136)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.39780 (    2)
  hydrogen bonds       : bond        0.04078 (  527)
  hydrogen bonds       : angle       4.26340 ( 1563)

*********************** 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
  120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7964 (tt)
REVERT: A  112 LYS cc_start: 0.7984 (tttt) cc_final: 0.7718 (tppt)
REVERT: A  182 MET cc_start: 0.8338 (tpp) cc_final: 0.7794 (ttt)
REVERT: A  227 GLN cc_start: 0.7975 (mt0) cc_final: 0.7584 (mm-40)
REVERT: A  305 LEU cc_start: 0.8034 (tp) cc_final: 0.7827 (mp)
REVERT: A  321 ASP cc_start: 0.7433 (p0) cc_final: 0.7195 (p0)
REVERT: A  433 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8269 (tp)
REVERT: B  182 MET cc_start: 0.8291 (tpp) cc_final: 0.8025 (ttt)
  outliers start: 32
  outliers final: 24
  residues processed: 108
  average time/residue: 0.0813
  time to fit residues: 12.3238
Evaluate side-chains
  107 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  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  433 LEU
Chi-restraints excluded: chain A residue  445 THR
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   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  445 THR
Chi-restraints excluded: chain B residue  520 VAL
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 86 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.193636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165211 restraints weight = 8786.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.165327 restraints weight = 6111.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.165306 restraints weight = 5149.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.166092 restraints weight = 5157.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.166201 restraints weight = 4837.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8199  Z= 0.158
  Angle     :  0.522   7.152  11138  Z= 0.273
  Chirality :  0.041   0.162   1382
  Planarity :  0.004   0.034   1378
  Dihedral  :  4.575  58.290   1130
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.56 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.26), residues: 1082
  helix:  1.29 (0.19), residues: 736
  sheet: -0.67 (0.87), residues: 56
  loop : -0.06 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 409 
 TYR   0.018   0.001   TYR B 216 
 PHE   0.012   0.001   PHE A  69 
 TRP   0.008   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8198)
  covalent geometry    : angle       0.52208 (11136)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.37769 (    2)
  hydrogen bonds       : bond        0.04184 (  527)
  hydrogen bonds       : angle       4.31875 ( 1563)

*********************** 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
  122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: A  112 LYS cc_start: 0.7965 (tttt) cc_final: 0.7666 (tppt)
REVERT: A  182 MET cc_start: 0.8325 (tpp) cc_final: 0.7822 (ttt)
REVERT: A  321 ASP cc_start: 0.7468 (p0) cc_final: 0.7235 (p0)
REVERT: A  433 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8270 (tp)
  outliers start: 28
  outliers final: 25
  residues processed: 110
  average time/residue: 0.0707
  time to fit residues: 11.5964
Evaluate side-chains
  118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  240 LEU
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  445 THR
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   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  445 THR
Chi-restraints excluded: chain B residue  520 VAL
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 59 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0370
   chunk 94 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
A 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.196448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.167783 restraints weight = 8782.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.168692 restraints weight = 6052.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.168508 restraints weight = 5083.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.168577 restraints weight = 4962.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.168687 restraints weight = 4946.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8199  Z= 0.130
  Angle     :  0.501   6.494  11138  Z= 0.263
  Chirality :  0.040   0.164   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.484  56.773   1130
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.26 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1082
  helix:  1.43 (0.19), residues: 740
  sheet: -0.61 (0.87), residues: 56
  loop : -0.10 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 355 
 TYR   0.015   0.001   TYR A 216 
 PHE   0.011   0.001   PHE A  69 
 TRP   0.010   0.002   TRP B 367 
 HIS   0.003   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8198)
  covalent geometry    : angle       0.50143 (11136)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.36426 (    2)
  hydrogen bonds       : bond        0.03779 (  527)
  hydrogen bonds       : angle       4.19058 ( 1563)

*********************** 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
  108 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7910 (tt)
REVERT: A  112 LYS cc_start: 0.7910 (tttt) cc_final: 0.7622 (tppt)
REVERT: A  182 MET cc_start: 0.8294 (tpp) cc_final: 0.7859 (ttt)
REVERT: A  321 ASP cc_start: 0.7444 (p0) cc_final: 0.7227 (p0)
REVERT: A  433 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (tt)
REVERT: B  112 LYS cc_start: 0.7882 (tttt) cc_final: 0.7618 (tppt)
  outliers start: 29
  outliers final: 23
  residues processed: 96
  average time/residue: 0.0812
  time to fit residues: 11.1801
Evaluate side-chains
  100 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  240 LEU
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   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  445 THR
Chi-restraints excluded: chain B residue  520 VAL
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 96 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 20 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.185289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.151600 restraints weight = 8679.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.155811 restraints weight = 5704.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.158523 restraints weight = 4394.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160019 restraints weight = 3696.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.161386 restraints weight = 3329.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8199  Z= 0.122
  Angle     :  0.498   6.600  11138  Z= 0.259
  Chirality :  0.040   0.146   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.453  56.156   1130
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.84 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.26), residues: 1082
  helix:  1.49 (0.19), residues: 740
  sheet: -0.57 (0.87), residues: 56
  loop : -0.12 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 409 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.010   0.002   TRP B 367 
 HIS   0.003   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8198)
  covalent geometry    : angle       0.49819 (11136)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.34207 (    2)
  hydrogen bonds       : bond        0.03631 (  527)
  hydrogen bonds       : angle       4.13306 ( 1563)

********************** 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
  96 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7923 (tt)
REVERT: A  112 LYS cc_start: 0.7887 (tttt) cc_final: 0.7577 (tppt)
REVERT: A  182 MET cc_start: 0.8266 (tpp) cc_final: 0.7918 (ttt)
REVERT: A  321 ASP cc_start: 0.7429 (p0) cc_final: 0.7206 (p0)
REVERT: A  433 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8179 (tt)
REVERT: B  112 LYS cc_start: 0.7902 (tttt) cc_final: 0.7572 (tppt)
REVERT: B  182 MET cc_start: 0.8321 (tpp) cc_final: 0.8003 (ttt)
  outliers start: 23
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0917
  time to fit residues: 11.5023
Evaluate side-chains
  94 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  240 LEU
Chi-restraints excluded: chain A residue  282 VAL
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   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  445 THR
Chi-restraints excluded: chain B residue  520 VAL
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 7 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 83 optimal weight:    0.4980
   chunk 103 optimal weight:    0.0970
   chunk 26 optimal weight:    7.9990
   chunk 5 optimal weight:    0.1980
   chunk 74 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.188486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153797 restraints weight = 8696.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158297 restraints weight = 5613.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160885 restraints weight = 4269.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.163030 restraints weight = 3599.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.164154 restraints weight = 3202.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8199  Z= 0.106
  Angle     :  0.477   6.806  11138  Z= 0.247
  Chirality :  0.040   0.143   1382
  Planarity :  0.003   0.033   1378
  Dihedral  :  4.351  54.845   1130
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 19.88 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.26), residues: 1082
  helix:  1.69 (0.19), residues: 744
  sheet: -0.08 (0.90), residues: 52
  loop : -0.15 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.012   0.001   TYR A 216 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.012   0.002   TRP B 367 
 HIS   0.004   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8198)
  covalent geometry    : angle       0.47751 (11136)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.27316 (    2)
  hydrogen bonds       : bond        0.03220 (  527)
  hydrogen bonds       : angle       3.98279 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1261.28 seconds
wall clock time: 22 minutes 32.91 seconds (1352.91 seconds total)