Starting phenix.real_space_refine
on Tue Jul 29 17:52:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jlq_22377/07_2025/7jlq_22377.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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      66      5.16       5
     C    7725      2.51       5
     N    1962      2.21       5
     O    1947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 99 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3900
          Classifications: {'peptide': 474}
          Link IDs: {'PTRANS': 17, 'TRANS': 456}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 7.40, per 1000 atoms: 0.63
  Number of scatterers: 11700
  At special positions: 0
  Unit cell: (130.41, 123.606, 92.988, 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      66     16.00
     O    1947      8.00
     N    1962      7.00
     C    7725      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  86 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  86 " - pdb=" SG  CYS C 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  86 " - pdb=" SG  CYS B 122 " 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: 3.10
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 9 sheets defined
      73.8% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 56
      removed outlier: 3.658A  pdb=" N   HIS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A  73 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 111 through 116'
    Processing helix  chain 'A' and resid 118 through 127
    Processing helix  chain 'A' and resid 132 through 166
      removed outlier: 3.852A  pdb=" N   ILE A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TRP A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLU A 159 " --> pdb=" O   CYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 179 through 190
      removed outlier: 3.514A  pdb=" N   THR A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 215 through 225
    Processing helix  chain 'A' and resid 244 through 256
    Processing helix  chain 'A' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG A 275 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY A 276 " --> pdb=" O   TYR A 273 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY A 277 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 317
      Proline residue:  A 302  - end of helix
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 324 through 328
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 367
    Processing helix  chain 'A' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL A 390 " --> pdb=" O   SER A 386 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 407 through 422
    Processing helix  chain 'A' and resid 435 through 446
      removed outlier: 3.711A  pdb=" N   ARG A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 453
      removed outlier: 3.820A  pdb=" N   GLN A 453 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 466
      removed outlier: 3.628A  pdb=" N   ARG A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 481
    Processing helix  chain 'A' and resid 481 through 493
      Proline residue:  A 487  - end of helix
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 497 through 508
      removed outlier: 3.546A  pdb=" N   ILE A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 56
      removed outlier: 3.658A  pdb=" N   HIS B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET B  62 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA B 115 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 111 through 116'
    Processing helix  chain 'B' and resid 118 through 127
    Processing helix  chain 'B' and resid 132 through 166
      removed outlier: 3.851A  pdb=" N   ILE B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU B 159 " --> pdb=" O   CYS B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 178
    Processing helix  chain 'B' and resid 179 through 190
      removed outlier: 3.516A  pdb=" N   THR B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
    Processing helix  chain 'B' and resid 215 through 225
    Processing helix  chain 'B' and resid 244 through 256
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY B 276 " --> pdb=" O   TYR B 273 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY B 277 " --> pdb=" O   LYS B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 317
      Proline residue:  B 302  - end of helix
    Processing helix  chain 'B' and resid 318 through 323
    Processing helix  chain 'B' and resid 324 through 328
    Processing helix  chain 'B' and resid 333 through 340
    Processing helix  chain 'B' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 367
    Processing helix  chain 'B' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL B 390 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
    Processing helix  chain 'B' and resid 407 through 422
    Processing helix  chain 'B' and resid 435 through 446
      removed outlier: 3.711A  pdb=" N   ARG B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS B 444 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 453
      removed outlier: 3.821A  pdb=" N   GLN B 453 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 466
      removed outlier: 3.628A  pdb=" N   ARG B 462 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 481
    Processing helix  chain 'B' and resid 481 through 493
      Proline residue:  B 487  - end of helix
    Processing helix  chain 'B' and resid 494 through 496
      No H-bonds generated for 'chain 'B' and resid 494 through 496'
    Processing helix  chain 'B' and resid 497 through 508
      removed outlier: 3.545A  pdb=" N   ILE B 502 " --> pdb=" O   ALA B 498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 56
      removed outlier: 3.659A  pdb=" N   HIS C  54 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 86
      removed outlier: 3.820A  pdb=" N   MET C  62 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE C  73 " --> pdb=" O   GLU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 116
      removed outlier: 4.336A  pdb=" N   ALA C 115 " --> pdb=" O   THR C 111 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE C 116 " --> pdb=" O   LEU C 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 111 through 116'
    Processing helix  chain 'C' and resid 118 through 127
    Processing helix  chain 'C' and resid 132 through 166
      removed outlier: 3.851A  pdb=" N   ILE C 138 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP C 143 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU C 159 " --> pdb=" O   CYS C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 178
    Processing helix  chain 'C' and resid 179 through 190
      removed outlier: 3.515A  pdb=" N   THR C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 213
    Processing helix  chain 'C' and resid 215 through 225
    Processing helix  chain 'C' and resid 244 through 256
    Processing helix  chain 'C' and resid 270 through 277
      removed outlier: 3.789A  pdb=" N   ARG C 275 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   GLY C 276 " --> pdb=" O   TYR C 273 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY C 277 " --> pdb=" O   LYS C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 317
      Proline residue:  C 302  - end of helix
    Processing helix  chain 'C' and resid 318 through 323
    Processing helix  chain 'C' and resid 324 through 328
    Processing helix  chain 'C' and resid 333 through 340
    Processing helix  chain 'C' and resid 346 through 357
      removed outlier: 3.632A  pdb=" N   ARG C 353 " --> pdb=" O   GLU C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 367
    Processing helix  chain 'C' and resid 370 through 398
      removed outlier: 3.581A  pdb=" N   VAL C 390 " --> pdb=" O   SER C 386 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP C 398 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 399 through 404
    Processing helix  chain 'C' and resid 407 through 422
    Processing helix  chain 'C' and resid 435 through 446
      removed outlier: 3.712A  pdb=" N   ARG C 439 " --> pdb=" O   GLU C 435 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS C 444 " --> pdb=" O   VAL C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 453
      removed outlier: 3.821A  pdb=" N   GLN C 453 " --> pdb=" O   ASP C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 466
      removed outlier: 3.627A  pdb=" N   ARG C 462 " --> pdb=" O   ARG C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 472 through 481
    Processing helix  chain 'C' and resid 481 through 493
      Proline residue:  C 487  - end of helix
    Processing helix  chain 'C' and resid 494 through 496
      No H-bonds generated for 'chain 'C' and resid 494 through 496'
    Processing helix  chain 'C' and resid 497 through 508
      removed outlier: 3.546A  pdb=" N   ILE C 502 " --> pdb=" O   ALA C 498 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234
    Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332
    Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512
    Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 234
    Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332
    Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512
    Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 234
    Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332
    Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512

    696 hydrogen bonds defined for protein.
    1971 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: 3.42

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3635
        1.34 -     1.46: 2515
        1.46 -     1.57: 5790
        1.57 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 12027
  Sorted by residual:
  bond pdb=" CA  PHE C 242 "
       pdb=" CB  PHE C 242 "
    ideal  model  delta    sigma   weight residual
    1.526  1.495  0.031 1.53e-02 4.27e+03 4.19e+00
  bond pdb=" CB  GLN B 120 "
       pdb=" CG  GLN B 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.15e+00
  bond pdb=" CB  GLN A 120 "
       pdb=" CG  GLN A 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.09e+00
  bond pdb=" CB  GLN C 120 "
       pdb=" CG  GLN C 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.573 -0.053 3.00e-02 1.11e+03 3.08e+00
  bond pdb=" CB  TRP B 332 "
       pdb=" CG  TRP B 332 "
    ideal  model  delta    sigma   weight residual
    1.498  1.446  0.052 3.10e-02 1.04e+03 2.79e+00
  ... (remaining 12022 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 15575
        2.05 -     4.10: 634
        4.10 -     6.15: 95
        6.15 -     8.20: 30
        8.20 -    10.25: 4
  Bond angle restraints: 16338
  Sorted by residual:
  angle pdb=" CB  GLN A 120 "
        pdb=" CG  GLN A 120 "
        pdb=" CD  GLN A 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.42   -6.82 1.70e+00 3.46e-01 1.61e+01
  angle pdb=" CB  GLN B 120 "
        pdb=" CG  GLN B 120 "
        pdb=" CD  GLN B 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.41   -6.81 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" CB  GLN C 120 "
        pdb=" CG  GLN C 120 "
        pdb=" CD  GLN C 120 "
      ideal   model   delta    sigma   weight residual
     112.60  119.40   -6.80 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" CA  GLN C 120 "
        pdb=" CB  GLN C 120 "
        pdb=" CG  GLN C 120 "
      ideal   model   delta    sigma   weight residual
     114.10  121.76   -7.66 2.00e+00 2.50e-01 1.47e+01
  angle pdb=" CA  GLN B 120 "
        pdb=" CB  GLN B 120 "
        pdb=" CG  GLN B 120 "
      ideal   model   delta    sigma   weight residual
     114.10  121.73   -7.63 2.00e+00 2.50e-01 1.46e+01
  ... (remaining 16333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 6291
       17.52 -    35.04: 579
       35.04 -    52.56: 114
       52.56 -    70.08: 18
       70.08 -    87.60: 15
  Dihedral angle restraints: 7017
    sinusoidal: 2832
      harmonic: 4185
  Sorted by residual:
  dihedral pdb=" CB  CYS C  86 "
           pdb=" SG  CYS C  86 "
           pdb=" SG  CYS C 122 "
           pdb=" CB  CYS C 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.71   33.71     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" CB  CYS B  86 "
           pdb=" SG  CYS B  86 "
           pdb=" SG  CYS B 122 "
           pdb=" CB  CYS B 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.69   33.69     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" CB  CYS A  86 "
           pdb=" SG  CYS A  86 "
           pdb=" SG  CYS A 122 "
           pdb=" CB  CYS A 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.69   33.69     1      1.00e+01 1.00e-02 1.61e+01
  ... (remaining 7014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 964
       0.036 -    0.071: 536
       0.071 -    0.107: 246
       0.107 -    0.143: 69
       0.143 -    0.178: 21
  Chirality restraints: 1836
  Sorted by residual:
  chirality pdb=" CB  ILE A 254 "
            pdb=" CA  ILE A 254 "
            pdb=" CG1 ILE A 254 "
            pdb=" CG2 ILE A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CB  ILE B 254 "
            pdb=" CA  ILE B 254 "
            pdb=" CG1 ILE B 254 "
            pdb=" CG2 ILE B 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CB  ILE C 254 "
            pdb=" CA  ILE C 254 "
            pdb=" CG1 ILE C 254 "
            pdb=" CG2 ILE C 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.71e-01
  ... (remaining 1833 not shown)

  Planarity restraints: 2031
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 180 "    0.018 2.00e-02 2.50e+03   1.77e-02 7.80e+00
        pdb=" CG  TRP C 180 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 180 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 180 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 180 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 180 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 180 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 180 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 180 "    0.019 2.00e-02 2.50e+03   1.76e-02 7.77e+00
        pdb=" CG  TRP A 180 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 180 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 180 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 180 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 180 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 180 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 180 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 180 "   -0.019 2.00e-02 2.50e+03   1.76e-02 7.76e+00
        pdb=" CG  TRP B 180 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 180 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 180 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 180 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 180 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 180 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 180 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 180 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2028 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 432
        2.70 -     3.25: 12051
        3.25 -     3.80: 18486
        3.80 -     4.35: 23424
        4.35 -     4.90: 38982
  Nonbonded interactions: 93375
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 209 "
            pdb=" OE2 GLU C 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OH  TYR A 209 "
            pdb=" OE2 GLU A 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OH  TYR B 209 "
            pdb=" OE2 GLU B 349 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" NH2 ARG B  49 "
            pdb=" OD1 ASN B 153 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" NH2 ARG A  49 "
            pdb=" OD1 ASN A 153 "
     model   vdw
     2.161 3.120
  ... (remaining 93370 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     29.130
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
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      :  0.007   0.053  12030  Z= 0.340
  Angle     :  0.990  10.250  16344  Z= 0.549
  Chirality :  0.054   0.178   1836
  Planarity :  0.005   0.029   2031
  Dihedral  : 14.269  87.601   4296
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  3.08 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.21), residues: 1410
  helix: -0.46 (0.16), residues: 942
  sheet: -2.13 (0.85), residues: 30
  loop : -2.63 (0.25), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP C 180 
 HIS   0.007   0.002   HIS A 451 
 PHE   0.040   0.003   PHE A 368 
 TYR   0.030   0.004   TYR A 471 
 ARG   0.005   0.001   ARG C 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20106 (  696)
  hydrogen bonds       : angle       6.50632 ( 1971)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.97087 (    6)
  covalent geometry    : bond        0.00712 (12027)
  covalent geometry    : angle       0.98979 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 411
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9175 (mt) cc_final: 0.8946 (tp)
REVERT: A   79 PHE cc_start: 0.8860 (t80) cc_final: 0.8492 (t80)
REVERT: A   83 LEU cc_start: 0.8269 (mt) cc_final: 0.7593 (mt)
REVERT: A  226 SER cc_start: 0.8013 (m) cc_final: 0.7732 (p)
REVERT: A  321 LYS cc_start: 0.7793 (tptm) cc_final: 0.7006 (mttt)
REVERT: A  363 LYS cc_start: 0.7773 (mttt) cc_final: 0.7507 (mttt)
REVERT: A  364 TYR cc_start: 0.8049 (t80) cc_final: 0.7783 (t80)
REVERT: A  435 GLU cc_start: 0.7716 (tp30) cc_final: 0.7239 (tp30)
REVERT: A  445 ILE cc_start: 0.6461 (pt) cc_final: 0.6249 (pt)
REVERT: B   83 LEU cc_start: 0.8230 (mt) cc_final: 0.7923 (mt)
REVERT: B  143 TRP cc_start: 0.8207 (t60) cc_final: 0.7709 (t60)
REVERT: B  152 TYR cc_start: 0.8314 (t80) cc_final: 0.8038 (t80)
REVERT: B  226 SER cc_start: 0.7959 (m) cc_final: 0.7738 (p)
REVERT: B  364 TYR cc_start: 0.7941 (t80) cc_final: 0.7738 (t80)
REVERT: B  372 LEU cc_start: 0.8949 (tp) cc_final: 0.8539 (mt)
REVERT: B  445 ILE cc_start: 0.6512 (pt) cc_final: 0.6279 (pt)
REVERT: B  471 TYR cc_start: 0.8585 (m-80) cc_final: 0.7338 (m-10)
REVERT: C   62 MET cc_start: 0.7010 (ttp) cc_final: 0.6662 (tmm)
REVERT: C  226 SER cc_start: 0.7880 (m) cc_final: 0.7679 (p)
REVERT: C  471 TYR cc_start: 0.8526 (m-80) cc_final: 0.8311 (m-10)
  outliers start: 9
  outliers final: 0
  residues processed: 416
  average time/residue: 0.2430
  time to fit residues: 141.0687
Evaluate side-chains
  228 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
B 406 HIS
C 406 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.172468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.134608 restraints weight = 16789.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.136125 restraints weight = 10491.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.137544 restraints weight = 8092.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6523
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12030  Z= 0.147
  Angle     :  0.685  11.518  16344  Z= 0.344
  Chirality :  0.043   0.171   1836
  Planarity :  0.005   0.047   2031
  Dihedral  :  4.236  16.329   1557
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.64 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.22), residues: 1410
  helix:  0.43 (0.17), residues: 942
  sheet: -1.44 (0.89), residues: 30
  loop : -2.04 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 143 
 HIS   0.005   0.001   HIS B 406 
 PHE   0.024   0.001   PHE B 475 
 TYR   0.015   0.002   TYR A 157 
 ARG   0.004   0.000   ARG B 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04841 (  696)
  hydrogen bonds       : angle       4.89842 ( 1971)
  SS BOND              : bond        0.01464 (    3)
  SS BOND              : angle       4.36385 (    6)
  covalent geometry    : bond        0.00317 (12027)
  covalent geometry    : angle       0.68032 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 263
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9248 (mt) cc_final: 0.8962 (tp)
REVERT: A   83 LEU cc_start: 0.8265 (mt) cc_final: 0.7998 (mt)
REVERT: A  310 LEU cc_start: 0.7213 (mt) cc_final: 0.6820 (mt)
REVERT: A  354 LEU cc_start: 0.8152 (mt) cc_final: 0.7922 (mp)
REVERT: A  471 TYR cc_start: 0.8428 (m-10) cc_final: 0.8162 (m-10)
REVERT: B  143 TRP cc_start: 0.8013 (t60) cc_final: 0.7421 (t60)
REVERT: B  422 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7533 (mtp180)
REVERT: B  471 TYR cc_start: 0.8469 (m-80) cc_final: 0.6969 (m-10)
REVERT: C   62 MET cc_start: 0.7253 (ttp) cc_final: 0.6519 (tmm)
REVERT: C   75 PHE cc_start: 0.7932 (t80) cc_final: 0.7649 (t80)
REVERT: C  172 MET cc_start: 0.7583 (ppp) cc_final: 0.7323 (ppp)
  outliers start: 36
  outliers final: 15
  residues processed: 288
  average time/residue: 0.2036
  time to fit residues: 86.6048
Evaluate side-chains
  233 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  457 HIS
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  193 GLU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 106 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 127 optimal weight:   10.0000
   chunk 116 optimal weight:    8.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 216 GLN
C  57 ASN
C 288 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.169455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.132195 restraints weight = 17257.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.135521 restraints weight = 10849.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.136436 restraints weight = 7471.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12030  Z= 0.156
  Angle     :  0.645  11.053  16344  Z= 0.329
  Chirality :  0.042   0.135   1836
  Planarity :  0.005   0.049   2031
  Dihedral  :  4.304  18.540   1557
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.72 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.22), residues: 1410
  helix:  0.61 (0.17), residues: 948
  sheet: -1.12 (0.90), residues: 30
  loop : -1.80 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 143 
 HIS   0.003   0.001   HIS A 194 
 PHE   0.022   0.001   PHE A  73 
 TYR   0.020   0.002   TYR C 157 
 ARG   0.003   0.000   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  696)
  hydrogen bonds       : angle       4.75522 ( 1971)
  SS BOND              : bond        0.01052 (    3)
  SS BOND              : angle       3.07137 (    6)
  covalent geometry    : bond        0.00343 (12027)
  covalent geometry    : angle       0.64193 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 238
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9238 (mt) cc_final: 0.8759 (tp)
REVERT: A   71 MET cc_start: 0.8480 (mtm) cc_final: 0.8048 (ptp)
REVERT: A  310 LEU cc_start: 0.7264 (mt) cc_final: 0.6934 (mt)
REVERT: A  354 LEU cc_start: 0.8343 (mt) cc_final: 0.8101 (mp)
REVERT: A  363 LYS cc_start: 0.7545 (mttt) cc_final: 0.7344 (mtmt)
REVERT: A  365 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6693 (mpp)
REVERT: A  435 GLU cc_start: 0.7432 (tp30) cc_final: 0.6873 (tp30)
REVERT: A  469 PHE cc_start: 0.7287 (t80) cc_final: 0.6110 (t80)
REVERT: B   81 THR cc_start: 0.8646 (p) cc_final: 0.8399 (t)
REVERT: B  143 TRP cc_start: 0.8007 (t60) cc_final: 0.7358 (t60)
REVERT: B  430 MET cc_start: 0.6904 (ptm) cc_final: 0.6700 (ptt)
REVERT: B  471 TYR cc_start: 0.8392 (m-80) cc_final: 0.7066 (m-10)
REVERT: C   66 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8614 (mm-30)
REVERT: C   71 MET cc_start: 0.8402 (mtm) cc_final: 0.8037 (ptp)
REVERT: C   75 PHE cc_start: 0.7688 (t80) cc_final: 0.7442 (t80)
REVERT: C   81 THR cc_start: 0.8718 (p) cc_final: 0.8464 (t)
REVERT: C  363 LYS cc_start: 0.7119 (mttt) cc_final: 0.6726 (mtmt)
REVERT: C  469 PHE cc_start: 0.7506 (t80) cc_final: 0.6843 (t80)
REVERT: C  471 TYR cc_start: 0.8361 (m-80) cc_final: 0.7005 (m-10)
  outliers start: 51
  outliers final: 29
  residues processed: 268
  average time/residue: 0.1942
  time to fit residues: 78.3042
Evaluate side-chains
  244 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  457 HIS
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 132 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 35 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 284 GLN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 ASN
** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 ASN
C 284 GLN
C 288 ASN
** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.172282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.136112 restraints weight = 17241.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.138240 restraints weight = 10344.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.139343 restraints weight = 7958.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12030  Z= 0.128
  Angle     :  0.631  12.704  16344  Z= 0.311
  Chirality :  0.041   0.129   1836
  Planarity :  0.004   0.044   2031
  Dihedral  :  4.220  18.721   1557
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.04 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.22), residues: 1410
  helix:  0.80 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -1.80 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 143 
 HIS   0.002   0.001   HIS A 194 
 PHE   0.022   0.001   PHE A  73 
 TYR   0.020   0.002   TYR B 157 
 ARG   0.003   0.000   ARG B 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  696)
  hydrogen bonds       : angle       4.61581 ( 1971)
  SS BOND              : bond        0.00999 (    3)
  SS BOND              : angle       2.64140 (    6)
  covalent geometry    : bond        0.00277 (12027)
  covalent geometry    : angle       0.62866 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 242
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9278 (mt) cc_final: 0.8119 (tp)
REVERT: A   71 MET cc_start: 0.8426 (mtm) cc_final: 0.8016 (ptp)
REVERT: A  310 LEU cc_start: 0.7327 (mt) cc_final: 0.6916 (mt)
REVERT: A  354 LEU cc_start: 0.8301 (mt) cc_final: 0.8059 (mp)
REVERT: A  363 LYS cc_start: 0.7505 (mttt) cc_final: 0.7201 (ttmt)
REVERT: A  365 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6713 (mpp)
REVERT: B   75 PHE cc_start: 0.7601 (t80) cc_final: 0.7222 (t80)
REVERT: B   81 THR cc_start: 0.8596 (p) cc_final: 0.8306 (t)
REVERT: B  164 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.7058 (t80)
REVERT: B  365 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6741 (mpp)
REVERT: B  471 TYR cc_start: 0.8445 (m-80) cc_final: 0.7076 (m-10)
REVERT: C   75 PHE cc_start: 0.7480 (t80) cc_final: 0.7116 (t80)
REVERT: C   81 THR cc_start: 0.8775 (p) cc_final: 0.8453 (t)
REVERT: C  363 LYS cc_start: 0.6908 (mttt) cc_final: 0.6450 (mtmt)
REVERT: C  365 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6738 (mpp)
REVERT: C  471 TYR cc_start: 0.8434 (m-80) cc_final: 0.7055 (m-10)
  outliers start: 48
  outliers final: 28
  residues processed: 270
  average time/residue: 0.2003
  time to fit residues: 80.4059
Evaluate side-chains
  243 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 211
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue  132 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  216 GLN
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  254 ILE
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 94 optimal weight:   20.0000
   chunk 103 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 61 optimal weight:    8.9990
   chunk 64 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 288 ASN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 HIS
B  57 ASN
** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 HIS
C  55 GLN
C  57 ASN
C 288 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.168660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.131625 restraints weight = 17595.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.134535 restraints weight = 10503.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.136393 restraints weight = 7025.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12030  Z= 0.161
  Angle     :  0.657  11.891  16344  Z= 0.330
  Chirality :  0.042   0.129   1836
  Planarity :  0.005   0.047   2031
  Dihedral  :  4.352  19.985   1557
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 20.85 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.22), residues: 1410
  helix:  0.71 (0.17), residues: 939
  sheet:  None (None), residues: 0
  loop : -1.54 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 158 
 HIS   0.003   0.001   HIS B 451 
 PHE   0.033   0.002   PHE B 251 
 TYR   0.019   0.002   TYR A 249 
 ARG   0.003   0.000   ARG B 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  696)
  hydrogen bonds       : angle       4.74217 ( 1971)
  SS BOND              : bond        0.00941 (    3)
  SS BOND              : angle       2.50927 (    6)
  covalent geometry    : bond        0.00357 (12027)
  covalent geometry    : angle       0.65536 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 238
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6436 (m-40)
REVERT: A   67 ILE cc_start: 0.9314 (mt) cc_final: 0.9050 (tp)
REVERT: A  164 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6811 (t80)
REVERT: A  354 LEU cc_start: 0.8396 (mt) cc_final: 0.8154 (mp)
REVERT: A  363 LYS cc_start: 0.7720 (mttt) cc_final: 0.7242 (ttmt)
REVERT: A  365 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.6649 (mpp)
REVERT: A  435 GLU cc_start: 0.7317 (tp30) cc_final: 0.6869 (tp30)
REVERT: A  469 PHE cc_start: 0.7456 (t80) cc_final: 0.6284 (t80)
REVERT: B   75 PHE cc_start: 0.7460 (t80) cc_final: 0.7138 (t80)
REVERT: B  164 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: B  251 PHE cc_start: 0.7282 (m-80) cc_final: 0.6910 (m-10)
REVERT: B  471 TYR cc_start: 0.8518 (m-80) cc_final: 0.7220 (m-10)
REVERT: C  135 ILE cc_start: 0.8896 (mp) cc_final: 0.8419 (tp)
REVERT: C  164 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7212 (t80)
REVERT: C  363 LYS cc_start: 0.7076 (mttt) cc_final: 0.6694 (mtmt)
REVERT: C  365 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6607 (mpp)
REVERT: C  469 PHE cc_start: 0.7631 (t80) cc_final: 0.7019 (t80)
REVERT: C  471 TYR cc_start: 0.8503 (m-80) cc_final: 0.7172 (m-10)
  outliers start: 59
  outliers final: 39
  residues processed: 268
  average time/residue: 0.2178
  time to fit residues: 85.5228
Evaluate side-chains
  257 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 212
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   57 ASN
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  379 ASN
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain C residue   39 HIS
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   69 GLU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  150 PHE
Chi-restraints excluded: chain C residue  164 TYR
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  448 MET
Chi-restraints excluded: chain C residue  455 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 138 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 128 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 140 optimal weight:    9.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  57 ASN
C 288 ASN
** C 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.169994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.134217 restraints weight = 17786.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.135279 restraints weight = 11211.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.136518 restraints weight = 8981.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12030  Z= 0.140
  Angle     :  0.636  13.218  16344  Z= 0.318
  Chirality :  0.041   0.133   1836
  Planarity :  0.004   0.052   2031
  Dihedral  :  4.315  16.950   1557
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 21.41 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1410
  helix:  0.67 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -1.49 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 158 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.038   0.001   PHE A 382 
 TYR   0.020   0.002   TYR C 157 
 ARG   0.003   0.000   ARG B 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  696)
  hydrogen bonds       : angle       4.70945 ( 1971)
  SS BOND              : bond        0.00921 (    3)
  SS BOND              : angle       2.33025 (    6)
  covalent geometry    : bond        0.00308 (12027)
  covalent geometry    : angle       0.63445 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 226
  time to evaluate  : 2.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9307 (mt) cc_final: 0.8945 (tp)
REVERT: A  164 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6637 (t80)
REVERT: A  354 LEU cc_start: 0.8329 (mt) cc_final: 0.8065 (mp)
REVERT: A  363 LYS cc_start: 0.7511 (mttt) cc_final: 0.7123 (ttmt)
REVERT: A  365 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6671 (mpp)
REVERT: A  435 GLU cc_start: 0.7267 (tp30) cc_final: 0.6957 (tp30)
REVERT: B   81 THR cc_start: 0.8495 (p) cc_final: 0.8235 (t)
REVERT: B  164 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7046 (t80)
REVERT: B  251 PHE cc_start: 0.7327 (m-80) cc_final: 0.6821 (m-10)
REVERT: B  363 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6859 (tttt)
REVERT: B  365 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6801 (mpp)
REVERT: B  471 TYR cc_start: 0.8564 (m-80) cc_final: 0.7309 (m-10)
REVERT: C   81 THR cc_start: 0.8603 (p) cc_final: 0.8397 (t)
REVERT: C  164 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7263 (t80)
REVERT: C  363 LYS cc_start: 0.6975 (mttt) cc_final: 0.6580 (mtmt)
REVERT: C  365 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6672 (mpp)
REVERT: C  469 PHE cc_start: 0.7704 (t80) cc_final: 0.7145 (t80)
REVERT: C  471 TYR cc_start: 0.8528 (m-80) cc_final: 0.7240 (m-10)
  outliers start: 58
  outliers final: 38
  residues processed: 259
  average time/residue: 0.2577
  time to fit residues: 100.0809
Evaluate side-chains
  255 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 210
  time to evaluate  : 1.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  379 ASN
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   40 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  150 PHE
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  293 ILE
Chi-restraints excluded: chain B residue  363 LYS
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  150 PHE
Chi-restraints excluded: chain C residue  164 TYR
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  400 ASP
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 84 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 125 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 17 optimal weight:    9.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 288 ASN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 GLN
B 436 GLN
C 288 ASN
C 344 ASN
C 436 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.173473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.135484 restraints weight = 17727.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.138161 restraints weight = 10465.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.140430 restraints weight = 7069.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12030  Z= 0.116
  Angle     :  0.623  11.929  16344  Z= 0.307
  Chirality :  0.041   0.177   1836
  Planarity :  0.004   0.052   2031
  Dihedral  :  4.204  20.121   1557
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 23.46 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.22), residues: 1410
  helix:  0.93 (0.17), residues: 951
  sheet:  None (None), residues: 0
  loop : -1.53 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 180 
 HIS   0.002   0.000   HIS C  54 
 PHE   0.035   0.001   PHE A 382 
 TYR   0.019   0.001   TYR A 339 
 ARG   0.005   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  696)
  hydrogen bonds       : angle       4.58260 ( 1971)
  SS BOND              : bond        0.00978 (    3)
  SS BOND              : angle       2.06881 (    6)
  covalent geometry    : bond        0.00240 (12027)
  covalent geometry    : angle       0.62151 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 1.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9293 (mt) cc_final: 0.9036 (tp)
REVERT: A   71 MET cc_start: 0.9011 (ptm) cc_final: 0.8780 (ptp)
REVERT: A  164 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6728 (t80)
REVERT: A  216 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7409 (mm-40)
REVERT: A  251 PHE cc_start: 0.7066 (m-10) cc_final: 0.6842 (m-80)
REVERT: A  354 LEU cc_start: 0.8339 (mt) cc_final: 0.8037 (mp)
REVERT: A  363 LYS cc_start: 0.7547 (mttt) cc_final: 0.7152 (ttmt)
REVERT: A  365 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6886 (mpp)
REVERT: B   81 THR cc_start: 0.8768 (p) cc_final: 0.8516 (t)
REVERT: B  164 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7133 (t80)
REVERT: B  251 PHE cc_start: 0.7272 (m-80) cc_final: 0.6761 (m-10)
REVERT: B  365 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7636 (mtp)
REVERT: C  226 SER cc_start: 0.8298 (t) cc_final: 0.7618 (p)
REVERT: C  251 PHE cc_start: 0.6987 (m-10) cc_final: 0.6744 (m-80)
REVERT: C  363 LYS cc_start: 0.6932 (mttt) cc_final: 0.6521 (mtmt)
REVERT: C  365 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6643 (mpp)
REVERT: C  471 TYR cc_start: 0.8473 (m-80) cc_final: 0.7163 (m-10)
  outliers start: 45
  outliers final: 27
  residues processed: 266
  average time/residue: 0.3359
  time to fit residues: 133.4051
Evaluate side-chains
  252 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 220
  time to evaluate  : 2.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 101 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 ASN
** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 GLN
B  72 GLN
B 406 HIS
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.172551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.134158 restraints weight = 17810.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.136181 restraints weight = 10516.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.137684 restraints weight = 7753.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12030  Z= 0.125
  Angle     :  0.650  13.742  16344  Z= 0.321
  Chirality :  0.042   0.239   1836
  Planarity :  0.005   0.079   2031
  Dihedral  :  4.219  18.889   1557
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 23.46 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1410
  helix:  0.82 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.49 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 143 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.045   0.001   PHE A 382 
 TYR   0.018   0.002   TYR B 157 
 ARG   0.012   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  696)
  hydrogen bonds       : angle       4.59139 ( 1971)
  SS BOND              : bond        0.00950 (    3)
  SS BOND              : angle       1.93722 (    6)
  covalent geometry    : bond        0.00276 (12027)
  covalent geometry    : angle       0.64944 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 225
  time to evaluate  : 3.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9275 (mt) cc_final: 0.8652 (tp)
REVERT: A   71 MET cc_start: 0.8990 (ptm) cc_final: 0.8452 (ptp)
REVERT: A  164 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6881 (t80)
REVERT: A  310 LEU cc_start: 0.7397 (mt) cc_final: 0.6905 (mt)
REVERT: A  354 LEU cc_start: 0.8418 (mt) cc_final: 0.8122 (mp)
REVERT: A  363 LYS cc_start: 0.7650 (mttt) cc_final: 0.7328 (mtmt)
REVERT: A  365 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.5908 (mpp)
REVERT: A  430 MET cc_start: 0.6664 (ptt) cc_final: 0.6278 (ptt)
REVERT: B   81 THR cc_start: 0.8913 (p) cc_final: 0.8650 (t)
REVERT: B   83 LEU cc_start: 0.7196 (mp) cc_final: 0.6798 (pp)
REVERT: B  164 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7160 (t80)
REVERT: B  330 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7158 (mtp85)
REVERT: B  363 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6825 (tttt)
REVERT: B  365 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.6906 (mpp)
REVERT: B  471 TYR cc_start: 0.8559 (m-80) cc_final: 0.7424 (m-10)
REVERT: C   62 MET cc_start: 0.7209 (tmm) cc_final: 0.6947 (tmm)
REVERT: C   83 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7734 (mt)
REVERT: C  226 SER cc_start: 0.8389 (t) cc_final: 0.7724 (p)
REVERT: C  251 PHE cc_start: 0.7021 (m-10) cc_final: 0.6773 (m-80)
REVERT: C  363 LYS cc_start: 0.7029 (mttt) cc_final: 0.6571 (mtmt)
REVERT: C  365 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6525 (mpp)
REVERT: C  448 MET cc_start: 0.6572 (pmm) cc_final: 0.6055 (pmm)
REVERT: C  471 TYR cc_start: 0.8476 (m-80) cc_final: 0.7177 (m-10)
  outliers start: 42
  outliers final: 26
  residues processed: 247
  average time/residue: 0.3469
  time to fit residues: 128.8457
Evaluate side-chains
  248 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 215
  time to evaluate  : 2.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  370 SER
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  363 LYS
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0470
   chunk 96 optimal weight:    8.9990
   chunk 88 optimal weight:    0.5980
   chunk 134 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.2880

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.172593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.134981 restraints weight = 17919.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.137146 restraints weight = 10532.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.138570 restraints weight = 7443.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.5494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12030  Z= 0.124
  Angle     :  0.661  14.555  16344  Z= 0.327
  Chirality :  0.042   0.239   1836
  Planarity :  0.004   0.058   2031
  Dihedral  :  4.216  18.537   1557
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.85 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1410
  helix:  0.81 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.44 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 143 
 HIS   0.003   0.000   HIS C 429 
 PHE   0.050   0.001   PHE A 382 
 TYR   0.018   0.002   TYR B 157 
 ARG   0.004   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  696)
  hydrogen bonds       : angle       4.57784 ( 1971)
  SS BOND              : bond        0.00901 (    3)
  SS BOND              : angle       1.89731 (    6)
  covalent geometry    : bond        0.00272 (12027)
  covalent geometry    : angle       0.66045 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 212
  time to evaluate  : 2.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9305 (mt) cc_final: 0.8682 (tp)
REVERT: A   71 MET cc_start: 0.8965 (ptm) cc_final: 0.8376 (ptp)
REVERT: A  164 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6815 (t80)
REVERT: A  209 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.5570 (m-10)
REVERT: A  310 LEU cc_start: 0.7390 (mt) cc_final: 0.6895 (mt)
REVERT: A  354 LEU cc_start: 0.8354 (mt) cc_final: 0.8060 (mp)
REVERT: A  363 LYS cc_start: 0.7425 (mttt) cc_final: 0.7028 (ttmt)
REVERT: A  365 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6471 (mpp)
REVERT: A  406 HIS cc_start: 0.6278 (OUTLIER) cc_final: 0.6044 (t70)
REVERT: A  430 MET cc_start: 0.6726 (ptt) cc_final: 0.6364 (ptt)
REVERT: B   72 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7952 (mm-40)
REVERT: B   81 THR cc_start: 0.8775 (p) cc_final: 0.8447 (t)
REVERT: B  164 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7116 (t80)
REVERT: B  363 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6883 (tttt)
REVERT: B  365 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6869 (mpp)
REVERT: C   62 MET cc_start: 0.7226 (tmm) cc_final: 0.6956 (tmm)
REVERT: C   83 LEU cc_start: 0.8064 (mt) cc_final: 0.7699 (mt)
REVERT: C  209 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.5712 (m-10)
REVERT: C  251 PHE cc_start: 0.7009 (m-10) cc_final: 0.6756 (m-80)
REVERT: C  363 LYS cc_start: 0.6989 (mttt) cc_final: 0.6553 (mtmt)
REVERT: C  365 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6571 (mpp)
REVERT: C  428 GLN cc_start: 0.8351 (mp10) cc_final: 0.8030 (mp10)
REVERT: C  448 MET cc_start: 0.6489 (pmm) cc_final: 0.5752 (pmm)
REVERT: C  480 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6142 (tt)
  outliers start: 44
  outliers final: 28
  residues processed: 235
  average time/residue: 0.2443
  time to fit residues: 85.2424
Evaluate side-chains
  246 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 208
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  209 TYR
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  164 TYR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  209 TYR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  363 LYS
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  209 TYR
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  370 SER
Chi-restraints excluded: chain C residue  379 ASN
Chi-restraints excluded: chain C residue  431 VAL
Chi-restraints excluded: chain C residue  480 LEU
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 106 optimal weight:    0.0060
   chunk 55 optimal weight:    0.0270
   chunk 116 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 134 optimal weight:    0.0570
   chunk 126 optimal weight:    0.0470
   chunk 61 optimal weight:    0.3980
   chunk 117 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0670
   overall best weight:    0.0408

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 288 ASN
B  57 ASN
B 288 ASN
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 ASN
C 429 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.178215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.141496 restraints weight = 17442.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.141949 restraints weight = 9435.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.142604 restraints weight = 7630.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.5805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12030  Z= 0.119
  Angle     :  0.664  14.393  16344  Z= 0.322
  Chirality :  0.041   0.260   1836
  Planarity :  0.004   0.062   2031
  Dihedral  :  4.097  18.396   1557
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 25.20 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.22), residues: 1410
  helix:  0.94 (0.17), residues: 957
  sheet:  None (None), residues: 0
  loop : -1.34 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 143 
 HIS   0.003   0.000   HIS C  54 
 PHE   0.018   0.001   PHE B 251 
 TYR   0.023   0.001   TYR B 157 
 ARG   0.007   0.000   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  696)
  hydrogen bonds       : angle       4.43738 ( 1971)
  SS BOND              : bond        0.00888 (    3)
  SS BOND              : angle       1.54888 (    6)
  covalent geometry    : bond        0.00244 (12027)
  covalent geometry    : angle       0.66388 (16338)

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

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

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2820 Ramachandran restraints generated.
    1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ILE cc_start: 0.9295 (mt) cc_final: 0.8679 (tp)
REVERT: A   71 MET cc_start: 0.8975 (ptm) cc_final: 0.8392 (ptp)
REVERT: A  164 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.7102 (t80)
REVERT: A  310 LEU cc_start: 0.7304 (mt) cc_final: 0.6818 (mt)
REVERT: A  324 PRO cc_start: 0.7918 (Cg_endo) cc_final: 0.7697 (Cg_exo)
REVERT: A  330 ARG cc_start: 0.7308 (mtt90) cc_final: 0.6522 (mtt-85)
REVERT: A  365 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.5920 (mpp)
REVERT: A  406 HIS cc_start: 0.6516 (OUTLIER) cc_final: 0.6229 (t70)
REVERT: A  430 MET cc_start: 0.6544 (ptt) cc_final: 0.5967 (ptt)
REVERT: A  463 ASP cc_start: 0.6702 (m-30) cc_final: 0.6071 (m-30)
REVERT: B   71 MET cc_start: 0.8055 (mtm) cc_final: 0.7855 (ptm)
REVERT: B   81 THR cc_start: 0.8853 (p) cc_final: 0.8548 (t)
REVERT: B  365 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.6775 (mpp)
REVERT: C   83 LEU cc_start: 0.8028 (mt) cc_final: 0.7707 (mt)
REVERT: C  209 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.5489 (m-10)
REVERT: C  226 SER cc_start: 0.8332 (t) cc_final: 0.7723 (p)
REVERT: C  251 PHE cc_start: 0.6998 (m-10) cc_final: 0.6598 (m-80)
REVERT: C  255 LEU cc_start: 0.7616 (mt) cc_final: 0.7199 (mp)
REVERT: C  330 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7136 (mtp85)
REVERT: C  363 LYS cc_start: 0.7059 (mttt) cc_final: 0.6613 (mtmt)
REVERT: C  365 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6595 (mpp)
REVERT: C  480 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.5917 (tt)
  outliers start: 31
  outliers final: 15
  residues processed: 262
  average time/residue: 0.2248
  time to fit residues: 85.4038
Evaluate side-chains
  234 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   90 ASP
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  164 TYR
Chi-restraints excluded: chain A residue  178 CYS
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  178 CYS
Chi-restraints excluded: chain C residue  209 TYR
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  480 LEU
Chi-restraints excluded: chain C residue  489 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 114 optimal weight:    0.4980
   chunk 76 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 99 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9990
   chunk 137 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 288 ASN
B  57 ASN
C  57 ASN
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 288 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.176260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.140699 restraints weight = 17570.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.141553 restraints weight = 11702.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.142873 restraints weight = 9737.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.5921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12030  Z= 0.124
  Angle     :  0.693  14.301  16344  Z= 0.339
  Chirality :  0.043   0.289   1836
  Planarity :  0.004   0.062   2031
  Dihedral  :  4.050  18.030   1557
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 25.91 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.22), residues: 1410
  helix:  0.96 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -1.27 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP C 143 
 HIS   0.003   0.000   HIS A 194 
 PHE   0.043   0.001   PHE B  75 
 TYR   0.024   0.002   TYR C 157 
 ARG   0.006   0.000   ARG A 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  696)
  hydrogen bonds       : angle       4.38808 ( 1971)
  SS BOND              : bond        0.00863 (    3)
  SS BOND              : angle       1.71212 (    6)
  covalent geometry    : bond        0.00270 (12027)
  covalent geometry    : angle       0.69258 (16338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4635.90 seconds
wall clock time: 86 minutes 40.21 seconds (5200.21 seconds total)