Starting phenix.real_space_refine
on Fri Aug 22 22:09:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9veb_64996/08_2025/9veb_64996.map"
  }
  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    5278      2.51       5
     N    1280      2.21       5
     O    1458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8046
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4023
          Classifications: {'peptide': 543}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 524}
          Unresolved chain links: 1
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.34, per 1000 atoms: 0.29
  Number of scatterers: 8046
  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    1458      8.00
     N    1280      7.00
     C    5278      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: 0.59
  Conformation dependent library (CDL) restraints added in 418.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  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: 0.30
  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: 1.37

  Time building geometry restraints manager: 0.81 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: 2500
        1.34 -     1.46: 1305
        1.46 -     1.57: 4327
        1.57 -     1.69: 0
        1.69 -     1.80: 58
  Bond restraints: 8190
  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 8185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 10688
        1.13 -     2.25: 326
        2.25 -     3.38: 68
        3.38 -     4.51: 26
        4.51 -     5.63: 12
  Bond angle restraints: 11120
  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 11115 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 4196
       14.85 -    29.71: 448
       29.71 -    44.56: 132
       44.56 -    59.42: 27
       59.42 -    74.27: 20
  Dihedral angle restraints: 4823
    sinusoidal: 1757
      harmonic: 3066
  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 4820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1001
       0.040 -    0.080: 281
       0.080 -    0.120: 82
       0.120 -    0.160: 10
       0.160 -    0.200: 4
  Chirality restraints: 1378
  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 1375 not shown)

  Planarity restraints: 1376
  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 1373 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1833
        2.78 -     3.31: 8073
        3.31 -     3.84: 13622
        3.84 -     4.37: 14949
        4.37 -     4.90: 26845
  Nonbonded interactions: 65322
  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 65317 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:             1.010
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.520
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.970
-------------------------------------------------------------------------------
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   8191  Z= 0.167
  Angle     :  0.529   5.632  11122  Z= 0.297
  Chirality :  0.041   0.200   1378
  Planarity :  0.004   0.030   1376
  Dihedral  : 14.492  74.272   2864
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 17.02 %
    Favored  : 82.75 %
  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:  0.91 (0.26), residues: 1076
  helix:  1.07 (0.19), residues: 736
  sheet: -0.40 (0.77), residues: 56
  loop : -0.16 (0.38), residues: 284

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        0.00292 ( 8190)
  covalent geometry    : angle       0.52868 (11120)
  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)
************************************************

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 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  : 0.279 
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: 0.6406 (mm-40)
REVERT: B  227 GLN cc_start: 0.6554 (mt0) cc_final: 0.6300 (mm-40)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0869
  time to fit residues: 9.9701
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  : 0.213 
-------------------------------------------------------------------------------
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:    5.9990
   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:    0.9586

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.187688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.154146 restraints weight = 8549.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.158759 restraints weight = 5394.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.161785 restraints weight = 4045.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.163677 restraints weight = 3350.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.164816 restraints weight = 2964.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.0811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8191  Z= 0.131
  Angle     :  0.483   6.051  11122  Z= 0.258
  Chirality :  0.040   0.132   1378
  Planarity :  0.004   0.033   1376
  Dihedral  :  4.568  58.842   1128
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.69 %
    Favored  : 81.93 %
  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:  1.14 (0.26), residues: 1076
  helix:  1.24 (0.19), residues: 740
  sheet: -0.48 (0.78), residues: 56
  loop : -0.06 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  76 
 TYR   0.011   0.001   TYR A 216 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.007   0.002   TRP B 367 
 HIS   0.003   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8190)
  covalent geometry    : angle       0.48259 (11120)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       0.68587 (    2)
  hydrogen bonds       : bond        0.03989 (  527)
  hydrogen bonds       : angle       4.39303 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7772 (tt)
REVERT: A  112 LYS cc_start: 0.7863 (tttt) cc_final: 0.7619 (tppt)
REVERT: A  182 MET cc_start: 0.8276 (tpp) cc_final: 0.8046 (ttt)
REVERT: A  203 MET cc_start: 0.7515 (mtt) cc_final: 0.7160 (mtp)
REVERT: B   20 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8057 (tt)
  outliers start: 29
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0649
  time to fit residues: 9.0528
Evaluate side-chains
  86 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  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  445 THR
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  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 89 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0970
   chunk 25 optimal weight:    0.8980
   chunk 83 optimal weight:    0.4980
   chunk 22 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 86 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5178

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.190063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.156156 restraints weight = 8497.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.160804 restraints weight = 5381.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.163493 restraints weight = 4052.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.165735 restraints weight = 3385.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.166862 restraints weight = 2988.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8191  Z= 0.111
  Angle     :  0.448   5.445  11122  Z= 0.240
  Chirality :  0.039   0.129   1378
  Planarity :  0.003   0.033   1376
  Dihedral  :  4.493  58.541   1128
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.57 %
    Favored  : 82.52 %
  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:  1.40 (0.26), residues: 1076
  helix:  1.43 (0.19), residues: 740
  sheet: -0.10 (0.85), residues: 52
  loop : -0.04 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  76 
 TYR   0.011   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.008   0.002   TRP B 367 
 HIS   0.002   0.000   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8190)
  covalent geometry    : angle       0.44808 (11120)
  SS BOND              : bond        0.00495 (    1)
  SS BOND              : angle       0.69534 (    2)
  hydrogen bonds       : bond        0.03605 (  527)
  hydrogen bonds       : angle       4.18685 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: A  112 LYS cc_start: 0.7863 (tttt) cc_final: 0.7606 (tppt)
REVERT: A  182 MET cc_start: 0.8286 (tpp) cc_final: 0.7798 (ttt)
REVERT: A  203 MET cc_start: 0.7502 (mtt) cc_final: 0.7194 (mtp)
REVERT: A  433 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8107 (tp)
REVERT: B   20 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8022 (tt)
REVERT: B  182 MET cc_start: 0.8139 (tpp) cc_final: 0.7931 (ttt)
REVERT: B  433 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8019 (tt)
  outliers start: 25
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0692
  time to fit residues: 9.3461
Evaluate side-chains
  86 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  164 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   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  282 VAL
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  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 102 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.185967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152773 restraints weight = 8732.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156844 restraints weight = 5650.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.159749 restraints weight = 4272.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161449 restraints weight = 3576.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.162701 restraints weight = 3184.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8191  Z= 0.137
  Angle     :  0.476   6.092  11122  Z= 0.253
  Chirality :  0.040   0.152   1378
  Planarity :  0.004   0.034   1376
  Dihedral  :  4.527  59.522   1128
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.69 %
    Favored  : 81.93 %
  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:  1.25 (0.26), residues: 1076
  helix:  1.34 (0.19), residues: 740
  sheet: -0.07 (0.87), residues: 52
  loop : -0.18 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.007   0.002   TRP B 367 
 HIS   0.004   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8190)
  covalent geometry    : angle       0.47623 (11120)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       0.40373 (    2)
  hydrogen bonds       : bond        0.03970 (  527)
  hydrogen bonds       : angle       4.21865 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7895 (tt)
REVERT: A  112 LYS cc_start: 0.7937 (tttt) cc_final: 0.7625 (tppt)
REVERT: A  182 MET cc_start: 0.8327 (tpp) cc_final: 0.7812 (ttt)
REVERT: A  186 MET cc_start: 0.7370 (mtm) cc_final: 0.7160 (mtp)
REVERT: A  321 ASP cc_start: 0.7435 (p0) cc_final: 0.7167 (p0)
REVERT: A  433 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (tp)
REVERT: B   20 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8114 (tt)
REVERT: B  433 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (tt)
  outliers start: 29
  outliers final: 21
  residues processed: 93
  average time/residue: 0.0720
  time to fit residues: 9.8220
Evaluate side-chains
  96 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   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  433 LEU
Chi-restraints excluded: chain B residue  482 MET
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 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 87 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.186609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.152938 restraints weight = 8613.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.157367 restraints weight = 5515.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160203 restraints weight = 4173.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161969 restraints weight = 3484.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.163257 restraints weight = 3089.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8191  Z= 0.121
  Angle     :  0.459   5.851  11122  Z= 0.244
  Chirality :  0.039   0.126   1378
  Planarity :  0.003   0.035   1376
  Dihedral  :  4.486  58.946   1128
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 15.50 %
    Favored  : 81.12 %
  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:  1.42 (0.26), residues: 1076
  helix:  1.50 (0.19), residues: 732
  sheet: -0.62 (0.74), residues: 66
  loop :  0.03 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  76 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.010   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        0.00270 ( 8190)
  covalent geometry    : angle       0.45870 (11120)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.32279 (    2)
  hydrogen bonds       : bond        0.03718 (  527)
  hydrogen bonds       : angle       4.13316 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7888 (tt)
REVERT: A  112 LYS cc_start: 0.7913 (tttt) cc_final: 0.7641 (tppt)
REVERT: A  182 MET cc_start: 0.8301 (tpp) cc_final: 0.7856 (ttt)
REVERT: A  186 MET cc_start: 0.7353 (mtm) cc_final: 0.7114 (mtp)
REVERT: A  235 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (ttpt)
REVERT: A  321 ASP cc_start: 0.7402 (p0) cc_final: 0.7185 (p0)
REVERT: A  433 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8181 (tt)
REVERT: B   20 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7876 (tt)
REVERT: B  203 MET cc_start: 0.7710 (mtt) cc_final: 0.7388 (mtp)
  outliers start: 29
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0786
  time to fit residues: 11.5062
Evaluate side-chains
  98 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  208 VAL
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   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  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0000
   chunk 56 optimal weight:    0.4980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.4137 r_free = 0.4137 target = 0.188225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154299 restraints weight = 8610.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.158721 restraints weight = 5436.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.161634 restraints weight = 4107.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.163255 restraints weight = 3430.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.164615 restraints weight = 3054.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8191  Z= 0.108
  Angle     :  0.445   6.032  11122  Z= 0.237
  Chirality :  0.039   0.148   1378
  Planarity :  0.003   0.032   1376
  Dihedral  :  4.407  58.725   1128
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.62 %
    Favored  : 81.82 %
  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:  1.50 (0.26), residues: 1076
  helix:  1.59 (0.19), residues: 746
  sheet: -0.60 (0.84), residues: 56
  loop : -0.18 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  76 
 TYR   0.013   0.001   TYR B 216 
 PHE   0.009   0.001   PHE A  69 
 TRP   0.009   0.002   TRP B 367 
 HIS   0.002   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8190)
  covalent geometry    : angle       0.44461 (11120)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.24017 (    2)
  hydrogen bonds       : bond        0.03397 (  527)
  hydrogen bonds       : angle       3.97914 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7860 (tt)
REVERT: A  112 LYS cc_start: 0.7926 (tttt) cc_final: 0.7641 (tppt)
REVERT: A  182 MET cc_start: 0.8255 (tpp) cc_final: 0.7872 (ttt)
REVERT: A  186 MET cc_start: 0.7312 (mtm) cc_final: 0.7062 (mtp)
REVERT: A  321 ASP cc_start: 0.7360 (p0) cc_final: 0.7137 (p0)
REVERT: A  433 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: B   20 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7899 (tt)
  outliers start: 22
  outliers final: 17
  residues processed: 92
  average time/residue: 0.0740
  time to fit residues: 9.9484
Evaluate side-chains
  92 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  482 MET
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 97 optimal weight:    0.8980
   chunk 107 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 82 optimal weight:    0.4980
   chunk 81 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 528 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.187988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153990 restraints weight = 8679.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.158528 restraints weight = 5479.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.161283 restraints weight = 4123.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.163326 restraints weight = 3434.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164422 restraints weight = 3029.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8191  Z= 0.111
  Angle     :  0.452   5.616  11122  Z= 0.241
  Chirality :  0.039   0.135   1378
  Planarity :  0.003   0.032   1376
  Dihedral  :  4.400  59.136   1128
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.97 %
    Favored  : 81.47 %
  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:  1.51 (0.26), residues: 1076
  helix:  1.61 (0.19), residues: 742
  sheet: -0.61 (0.84), residues: 56
  loop : -0.18 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 409 
 TYR   0.013   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.008   0.002   TRP B 367 
 HIS   0.002   0.000   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8190)
  covalent geometry    : angle       0.45180 (11120)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.26036 (    2)
  hydrogen bonds       : bond        0.03416 (  527)
  hydrogen bonds       : angle       3.96458 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7875 (tt)
REVERT: A  112 LYS cc_start: 0.7888 (tttt) cc_final: 0.7606 (tppt)
REVERT: A  182 MET cc_start: 0.8236 (tpp) cc_final: 0.7859 (ttt)
REVERT: A  186 MET cc_start: 0.7313 (mtm) cc_final: 0.7059 (mtp)
REVERT: A  321 ASP cc_start: 0.7361 (p0) cc_final: 0.7128 (p0)
REVERT: A  433 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: B   20 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7886 (tt)
REVERT: B  112 LYS cc_start: 0.7839 (tttt) cc_final: 0.7597 (tppt)
  outliers start: 22
  outliers final: 17
  residues processed: 92
  average time/residue: 0.0708
  time to fit residues: 9.4732
Evaluate side-chains
  95 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   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  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.4980
   chunk 92 optimal weight:    0.0040
   chunk 20 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 528 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.188864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155258 restraints weight = 8549.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.159719 restraints weight = 5418.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.162488 restraints weight = 4088.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.164513 restraints weight = 3401.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.165475 restraints weight = 3020.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8191  Z= 0.105
  Angle     :  0.450   7.067  11122  Z= 0.238
  Chirality :  0.039   0.134   1378
  Planarity :  0.003   0.032   1376
  Dihedral  :  4.372  58.972   1128
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.08 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.63 (0.26), residues: 1076
  helix:  1.70 (0.19), residues: 746
  sheet: -0.63 (0.85), residues: 56
  loop : -0.12 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 409 
 TYR   0.012   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.009   0.002   TRP B 367 
 HIS   0.003   0.000   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8190)
  covalent geometry    : angle       0.45016 (11120)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.20323 (    2)
  hydrogen bonds       : bond        0.03263 (  527)
  hydrogen bonds       : angle       3.89606 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 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: 22
    poor density    : 76
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7847 (tt)
REVERT: A  112 LYS cc_start: 0.7864 (tttt) cc_final: 0.7565 (tppt)
REVERT: A  182 MET cc_start: 0.8227 (tpp) cc_final: 0.7877 (ttt)
REVERT: A  186 MET cc_start: 0.7327 (mtm) cc_final: 0.7060 (mtp)
REVERT: A  321 ASP cc_start: 0.7341 (p0) cc_final: 0.7108 (p0)
REVERT: A  433 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8118 (tt)
REVERT: B   20 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7864 (tt)
REVERT: B  112 LYS cc_start: 0.7827 (tttt) cc_final: 0.7569 (tppt)
  outliers start: 22
  outliers final: 18
  residues processed: 91
  average time/residue: 0.0829
  time to fit residues: 10.9207
Evaluate side-chains
  94 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.187517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.153662 restraints weight = 8579.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158007 restraints weight = 5500.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160857 restraints weight = 4159.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.162596 restraints weight = 3481.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.163459 restraints weight = 3098.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8191  Z= 0.116
  Angle     :  0.461   5.718  11122  Z= 0.245
  Chirality :  0.039   0.130   1378
  Planarity :  0.003   0.032   1376
  Dihedral  :  4.381  59.504   1128
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.85 %
    Favored  : 81.24 %
  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:  1.57 (0.26), residues: 1076
  helix:  1.70 (0.19), residues: 742
  sheet: -0.60 (0.86), residues: 56
  loop : -0.28 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 409 
 TYR   0.013   0.001   TYR B 216 
 PHE   0.010   0.001   PHE A  69 
 TRP   0.007   0.001   TRP B 367 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8190)
  covalent geometry    : angle       0.46139 (11120)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.25208 (    2)
  hydrogen bonds       : bond        0.03462 (  527)
  hydrogen bonds       : angle       3.95076 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7893 (tt)
REVERT: A  112 LYS cc_start: 0.7906 (tttt) cc_final: 0.7633 (tppt)
REVERT: A  182 MET cc_start: 0.8231 (tpp) cc_final: 0.7834 (ttt)
REVERT: A  186 MET cc_start: 0.7288 (mtm) cc_final: 0.7023 (mtp)
REVERT: A  321 ASP cc_start: 0.7373 (p0) cc_final: 0.7147 (p0)
REVERT: A  433 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8160 (tt)
REVERT: B   20 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7952 (tt)
REVERT: B  112 LYS cc_start: 0.7863 (tttt) cc_final: 0.7613 (tppt)
  outliers start: 25
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0814
  time to fit residues: 10.4947
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  : 0.301 
-------------------------------------------------------------------------------
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  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 48 optimal weight:    8.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.184274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150250 restraints weight = 8694.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.154530 restraints weight = 5648.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.156999 restraints weight = 4312.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158962 restraints weight = 3643.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.159801 restraints weight = 3256.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8191  Z= 0.137
  Angle     :  0.496   6.372  11122  Z= 0.261
  Chirality :  0.040   0.128   1378
  Planarity :  0.003   0.032   1376
  Dihedral  :  4.486  60.234   1128
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.50 %
    Favored  : 81.47 %
  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: 1076
  helix:  1.55 (0.19), residues: 738
  sheet: -0.62 (0.77), residues: 66
  loop : -0.48 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.018   0.001   TYR A 216 
 PHE   0.011   0.001   PHE B  69 
 TRP   0.005   0.002   TRP B 367 
 HIS   0.003   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8190)
  covalent geometry    : angle       0.49570 (11120)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.29291 (    2)
  hydrogen bonds       : bond        0.03885 (  527)
  hydrogen bonds       : angle       4.10490 ( 1563)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7967 (tt)
REVERT: A  112 LYS cc_start: 0.7928 (tttt) cc_final: 0.7639 (tppt)
REVERT: A  182 MET cc_start: 0.8296 (tpp) cc_final: 0.7793 (ttt)
REVERT: A  321 ASP cc_start: 0.7420 (p0) cc_final: 0.7202 (p0)
REVERT: A  433 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8186 (tp)
REVERT: B   20 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8002 (tt)
REVERT: B  112 LYS cc_start: 0.7895 (tttt) cc_final: 0.7598 (tppt)
  outliers start: 26
  outliers final: 22
  residues processed: 100
  average time/residue: 0.0938
  time to fit residues: 13.2770
Evaluate side-chains
  102 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  208 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue   88 PHE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  482 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.186234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152163 restraints weight = 8641.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156528 restraints weight = 5551.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.159268 restraints weight = 4228.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.161089 restraints weight = 3541.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.162309 restraints weight = 3152.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8191  Z= 0.122
  Angle     :  0.483   6.055  11122  Z= 0.256
  Chirality :  0.039   0.129   1378
  Planarity :  0.003   0.035   1376
  Dihedral  :  4.448  59.290   1128
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.55 %
    Favored  : 80.54 %
  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:  1.46 (0.26), residues: 1076
  helix:  1.64 (0.19), residues: 742
  sheet: -0.63 (0.76), residues: 66
  loop : -0.40 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 409 
 TYR   0.015   0.001   TYR A 216 
 PHE   0.010   0.001   PHE B  69 
 TRP   0.008   0.002   TRP B 367 
 HIS   0.002   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8190)
  covalent geometry    : angle       0.48312 (11120)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.17356 (    2)
  hydrogen bonds       : bond        0.03570 (  527)
  hydrogen bonds       : angle       4.01808 ( 1563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1258.59 seconds
wall clock time: 22 minutes 29.07 seconds (1349.07 seconds total)